# Patent

## Title
Differential enzymatic fragmentation

## Abstract

The present invention provides methods for detecting the presence of methylation at a locus within a population of nucleic acids.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is related to U.S. patent application Ser. No. 10/971,986, filed Oct. 21, 2004 and claims the benefit of U.S. Patent Application Nos. 60/513,426, filed Oct. 21, 2003, 60/561,721, filed Apr., 12, 2004, and 60/561,563, filed Apr. 12, 2004, the disclosures of each of which are hereby incorporated by reference in their entirety for all purposes.


BACKGROUND OF THE INVENTION
DNA typically comprises both methylated and unmethylated bases. Prokaryotic DNA is methylated at cytosine and adenosine residues (see, e.g., McClelland et al., Nuc. Acids. Res. 22:3640-3659 (1994). Methylation of prokaryotic DNA protects the DNA from digestion by cognate restriction enzymes, i.e., foreign DNAs (which are not methylated in this manner) that are introduced into the cell are degraded by restriction enzymes which cannot degrade the methylated prokaryotic DNA. DNA methylation patterns can be used to identify specific bacterial types (e.g., genus, species, strains, and isolates)
Mammalian DNA can only be methylated at cytosine residues, typically these cytosines are 5′ neighbors of guanine (CpG). This methylation has been shown by several lines of evidence to play a role in gene activity, cell differentiation, tumorigenesis, X-chromosome inactivation, genomic imprinting and other major biological processes (Razin and Riggs eds. in DNA Methylation Biochemistry and Biological Significance, Springer-Verlag, N.Y., 1984).
In eukaryotic cells, methylation of cytosine residues that are immediately 5′ to a guanosine, occurs predominantly in CG poor loci (Bird, Nature 321:209 (1986)). In contrast, discrete regions of CG dinucleotides called CpG islands remain unmethylated in normal cells, except during X-chromosome inactivation and parental specific imprinting (Li, et al., Nature 366:362 (1993)) where methylation of 5′ regulatory regions can lead to transcriptional repression.
Aberrant methylation, including aberrant methylation at specific loci, is often associated with a disease state. For example, de novo methylation of the Rb gene has been demonstrated in a small fraction of retinoblastomas (Sakai, et al., Am. J. Hum. Genet., 48:880 (1991)), and a more detailed analysis of the VHL gene showed aberrant methylation in a subset of sporadic renal cell carcinomas (Herman, et al., PNAS USA, 91:9700 (1994)). Expression of a tumor suppressor gene can also be abolished by de novo DNA methylation of a normally unmethylated 5′ CpG island. See, e.g., Issa, et al., Nature Genet. 7:536 (1994); Merlo, et al., Nature Med. 1:686 (1995); Herman, et al., Cancer Res., 56:722 (1996); Graff, et al., Cancer Res., 55:5195 (1995); Herman, et al., Cancer Res. 55:4525 (1995). Methylation of the p16 locus is associated with pancreatic cancer. See, e.g., Schutte et al., Cancer Res. 57:3126-3131 (1997). Methylation changes at the insulin-like growth factor II/H19 locus in kidney are associated with Wilms tumorigenesis. See, e.g., Okamoto et al., PNAS USA 94:5367-5371 (1997). The association of alteration of methylation in the p15, E-cadherin and von Hippel-Lindau loci are also associated with cancers. See, e.g., Herman et al., PNAS USA 93:9821-9826 (1997). The methylation state of GSTP1 is associated with prostate cancer. See, e.g., U.S. Pat. No. 5,552,277. Therefore, detection of altered methylation profiles at loci where such alterations are associated with disease can be used to provide diagnoses or prognoses of disease.
Current methods for determining whether DNA is methylated or unmethylated typically used methylation-sensitive restriction enzymes or a combination of methylation-sensitive and methylation-insensitive restriction enzymes (see, e.g., Burman et al., Am. J. Hum. Genet. 65:1375-1386 (1999); Toyota et al., Cancer Res. 59:2307-2312 (1999); Frigola et al., Nucleic Acids Res. 30(7):e28 (2002); Steigerwald et al., Nucleic Acids Res. 18(6):1435-1439 (1990); WO 03/038120; and U.S. patent Publication No. 2003/0129602 A1). In these methods, methylated DNA sequences remain intact for analysis.
Thus, there is a need in the art for more efficient methods of detecting methylation of DNA, particularly DNA at specific loci. The present invention addresses these and other needs.
BRIEF SUMMARY OF THE INVENTION
The present invention provides methods of detecting methylation at a locus within a population of nucleic acids using a methylation-dependent restriction enzyme, a methylation sensitive restriction enzyme, and/or a methylation-insensitive restriction enzyme.
One embodiment of the invention provides a method of detecting the presence of methylation at a locus within a population of nucleic acids by (a) dividing the population of nucleic acids into at least two portions, (b) contacting a first portion with a methylation-sensitive restriction enzyme to obtain a population comprising fragmented unmethylated copies of the locus and intact methylated copies of the locus; (c) quantifying the intact copies of the locus in the first portion; (d) contacting a second portion with a methylation-dependent restriction enzyme to obtain a population comprising fragmented methylated copies of the locus and intact unmethylated copies of the locus; (e) quantifying the intact copies of the locus in the second portion; and (f) determining the presence of methylation at the locus by comparing the number of intact copies of the locus in the first portion and number of intact copies of the locus in the second portion. In some embodiments, the method further comprises quantifying a third portion of the nucleic acids, thereby amplifying the total intact copies of the locus in the population; and comparing the number of total intact copies of the locus to the number of intact copies of the locus in the first portion and/or intact copies of the locus in the second portion. In some embodiments, the method further comprises contacting a third portion of the nucleic acids with a methylation-dependent restriction enzyme and a methylation-sensitive restriction enzyme; quantifying copies of the intact locus in the third portion; and determining the presence of methylation at the locus by comparing the number of the intact copies of the locus in the third portion to the number of intact copies of the locus in the first portion and/or intact unmethylated copies of the locus in the second portion. In some embodiments the second portion is also contacted with the methylation-sensitive restriction enzyme prior to the step of quantifying the intact copies of the locus in the second portion. In some embodiments, the first portion is also contacted with the methylation-dependent restriction enzyme prior to the step of quantifying the intact copies of the locus in the first portion. In some embodiments, the method further comprises contacting a fourth portion of the nucleic acids with a methylation-dependent restriction enzyme and a methylation-sensitive restriction enzyme; quantifying intact copies of the locus in the fourth portion; and determining the presence of methylation at the locus by comparing the number of intact copies of the locus in the fourth portion to the number of total intact copies of the locus in the third portion and/or intact copies of the locus in the first portion and/or intact copies of the locus in the second portion. In some embodiments, the method further comprises identification of mutations within the locus. In one embodiment, the method further comprises contacting a fifth portion of the nucleic acids with a methylation-insensitive restriction enzyme; quantifying intact copies of the locus in the fifth portion to obtain a population of nucleic acids comprising a mutation at the locus; and determining the presence of a mutation at the locus by comparing the number of the intact copies of the locus in the fifth portion to the number of intact copies of the locus in the fourth portion and/or total intact copies of the locus in the third portion and/or intact copies of the locus in the first portion and/or intact copies of the locus in the second portion.
In some embodiments, the number of unmethylated copies of the locus is determined by subtracting the number of intact copies of the locus remaining after the first portion is cut with the methylation-sensitive restriction enzyme from the total intact copies of the locus. In some embodiments, the number of methylated copies of the locus is determined by subtracting the number of intact copies of the locus remaining after the second portion is cut with the methylation-dependent restriction enzyme from the total intact copies of the locus. In some embodiments, the number of hemimethylated and mutant copies of the locus is determined by (a) subtracting the number of intact copies of the locus remaining after the first portion is cut with the methylation-sensitive restriction enzyme from the total intact copies of the locus, thereby determining the number of unmethylated copies of the locus; and (b) subtracting the number of unmethylated copies of the locus from the number of intact copies of the locus remaining after the second portion is cut with the methylation-dependent restriction enzyme, thereby determining the number of hemimethylated and mutant copies of the locus. In some embodiments, the number of hemimethylated and mutant copies of the locus is determined by: (a) subtracting the number of intact copies of the locus remaining after the second portion is cut with the methylation-dependent restriction enzyme from the total intact copies of the locus, thereby determining the number of methylated copies of the locus; and (b) subtracting the number of methylated copies of the locus from the number of intact copies of the locus remaining after the first portion is cut with the methylation-sensitive restriction enzyme, thereby determining the number of hemimethylated and mutant copies of the locus. In some embodiments the number of methylated and unmethylated copies of the locus is determined by subtracting the number of intact copies of the locus remaining after the fourth portion is cut with the methylation-dependent restriction enzyme and the methylation-sensitive restriction enzyme from the total intact copies of the locus, thereby determining the number of methylated and unmethylated copies of the locus. In some embodiments, the number of hemimethylated copies of the locus is determined by subtracting the number of intact loci remaining after the fifth portion of the nucleic acids is contacted with a methylation-insensitive restriction enzyme from the number of intact copies of the locus remaining after the fourth portion is cut with the methylation-dependent restriction enzyme and the methylation-sensitive restriction enzyme. In some embodiments, the number of methylated copies of the locus is determined by (a) subtracting the number of intact copies of the locus remaining after the fifth portion of the nucleic acids is contacted with a methylation-insensitive restriction enzyme from the number of intact copies of the locus remaining after the fourth portion is cut with the methylation-dependent restriction enzyme and the methylation-sensitive restriction enzyme, thereby determining the number of hemimethylated copies of the locus; and (b) subtracting the number of hemimethylated copies of the locus and the number of intact copies of the locus remaining after the fifth portion of the nucleic acids is contacted with the methylation-insensitive restriction enzyme from the number of intact copies of the locus remaining after the first portion of nucleic acids is contacted with the methylation-sensitive restriction enzyme, thereby determining the number of methylated copies of the locus. In some embodiments, the number of unmethylated copies of the locus is determined by (a) subtracting the number of intact copies of the locus remaining after the fifth portion of the nucleic acids is contacted with a methylation-insensitive restriction enzyme from the number of intact copies of the locus remaining after the fourth portion is cut with the methylation-dependent restriction enzyme and the methylation-sensitive restriction enzyme, thereby determining the number of hemimethylated copies of the locus; and (b) subtracting the number of hemimethylated copies of the locus and the number of intact copies of the locus remaining after the fifth portion of the nucleic acids is contacted with the methylation-insensitive restriction enzyme from the number of intact copies of the locus remaining after the second portion of nucleic acids is contacted with the methylation-dependent restriction enzyme, thereby determining the number of unmethylated copies of the locus.
In some embodiments, the quantifying steps comprise the direct detection of intact copies of locus with hybrid capture. In some embodiments, the quantifying steps comprise quantitative amplification including, e.g., quantitative PCR. In some embodiments, the quantitative amplification product is detected by detecting a label intercalated between bases of double stranded DNA sequences. In some embodiments, the quantitative amplification product is detected by detecting hybridization of a detectably labeled oligonucleotide to the amplification product. In some embodiments, the detectably labeled oligonucleotide is a labeled oligonucleotide probe comprising a fluorophore and a hairpin structure or a dual labeled oligonucleotide probe comprising a pair of interactive labels (e.g., a quencher and a fluorophore). In some embodiments, the fluorophore is activated to generate a detectable signal when the probe hybridizes to its target nucleic acid sequence. In some embodiments, the fluorophore is activated to generate a detectable signal when the probe hybridizes to its target nucleic acid sequence and an enzyme with 5′ exonuclease activity cleaves the portion of the probe comprising the quencher.
In some embodiments, the nucleic acids are contacted with an agent that modifies unmethylated cytosines before the amplification step; and the intact copies of the locus are amplified with a pair of oligonucleotide primers comprising at least one primer that distinguishes between modified methylated and unmethylated DNA.
In some embodiments, the nucleic acids are contacted with an agent (e.g., sodium bisulfite) that modifies unmethylated cytosines before the amplification step; and the intact copies of the locus are amplified with a pair of oligonucleotide primers comprising at least one primer that distinguishes between the protected methylated and the modified unmethylated DNA.
In some embodiments, the methylation-dependent restriction enzyme is contacted to the second, third, or fourth portion under conditions that allow for at least some copies of potential restriction enzyme cleavage sites for the methylation-dependent restriction enzyme in the locus to remain uncleaved. In some embodiments, the density of methylation at the locus is determined by comparing the number of intact methylated loci in the second, third, or fourth portion after cleavage with a control value representing the quantity of methylation in a control DNA.
In some embodiments, the methylation-sensitive restriction enzyme is contacted to the first or third portion under conditions that allow for at least some copies of potential restriction enzyme cleavage sites for the methylation-sensitive restriction enzyme in the locus to remain uncleaved. In some embodiments, the density of methylation at the locus is determined by comparing the number of intact unmethylated loci in the first or third portion after cleavage with a control value representing the quantity of methylation in a control DNA.
In some embodiments, the methylation is at the C4 position of a cytosine, the C5 position of a cytosine within the locus, or at the N6 position of an adenosine within the locus.
In some embodiments, the nucleic acids are DNA, including, e.g., genomic DNA.
In some embodiments, the methylation-sensitive restriction enzyme does not cut when a cytosine within the recognition sequence is methylated at position C5.
In some embodiments, the methylation-sensitive restriction enzyme is Aat II, Aci I, Acl I, Age I, Alu I, Asc I, Ase I, AsiS I, Bbe I, BsaA I, BsaH I, BsiE I, BsiW I, BsrF I, BssH II, BssK I, BstB I, BstN I, BstU I, Cla I, Eae I, Eag I, Fau I, Fse I, Hha I, HinP1 I, HinC II, Hpa II, Hpy99 I, HpyCH4 IV, Kas I, Mbo I, Mlu I, MapA1 I, Msp I, Nae I, Nar I, Not I, Pml I, Pst I, Pvu I, Rsr II, Sac II, Sap I, Sau3A I, Sfl I, Sfo I, SgrA I, Sma I, SnaB I, Tsc I, Xma I, and Zra I.
In some embodiments, the methylation-sensitive restriction enzyme does not cut when an adenosine within the recognition sequence is methylated at position N6.
In some embodiments, the methylation-sensitive restriction enzyme is Mbo I.
In some embodiments, the methylation-dependent restriction enzyme is McrBC, McrA, MrrA, or Dpn I.
In some embodiments, the first portion of genomic nucleic acids is further contacted with at least a second methylation-sensitive restriction enzyme.
In some embodiments, the second portion of genomic nucleic acids is further contacted with at least a second methylation-dependent restriction enzyme.
In some embodiments, the methylation-sensitive restriction enzyme is methyl-adenosine sensitive. In some embodiments, the methylation-sensitive restriction enzyme is methyl-cytosine sensitive.
In some embodiments, the methods further comprise contacting a third portion of the nucleic acids with a second methylation-sensitive restriction enzyme and contacting a fourth portion of the nucleic acids with a second methylation-dependent restriction enzyme; quantifying intact loci in the third and fourth portions; and determining the presence of methylation at the locus by comparing the number of intact copies of the locus in the third and fourth portions to the number of total intact copies of the locus and/or intact methylated copies of the locus and/or intact unmethylated copies of the locus. In some embodiments, the first methylation-sensitive restriction enzyme is methyl-cytosine sensitive; the second methylation-sensitive restriction enzyme is methyl-adenosine sensitive; the first methylation-dependent restriction enzyme is methyl-cytosine sensitive; and the second methylation dependent enzyme is methyl-adenosine sensitive.
In some embodiments, the presence of methylation at the locus is compared between at least two nucleic acid samples (e.g., isolated from at least two organisms having the same phenotype or a different phenotype). In some embodiments, the methods comprise quantifying the intact methylated copies of the locus in a first sample and a second sample; and comparing the quantity of amplified products from the two samples, thereby determining relative methylation at the locus between the two samples. In some embodiments, a first nucleic acid sample is isolated from a cell suspected of being a cancer cell and a second nucleic acid sample is isolated from a non-cancerous cell.
In some embodiments, the presence of methylation at two or more loci is determined by quantifying copies of intact DNA at the two different loci from a first portion contacted with a methylation-dependent restriction enzyme; quantifying the intact DNA as the two loci from a second portion contacted with a methylation-sensitive restriction enzyme; and comparing the quantities of the amplified products for the two loci.
In some embodiments, the population of nucleic acids is isolated from a cell, including, e.g., a plant cell, a fungal cell, a prokaryotic cell, an animal cell, a mammalian cell, or a cancer cell.
In some embodiments, the population of nucleic acids is isolated from a sample from a subject (e.g., a human), including, e.g., a body fluid, a secretion, or a tissue biopsy. In some embodiments, the subject is suspected of having cancer.
In some embodiments, the locus comprises a sequence that is more methylated in diseased cells than in non-diseased cells. In some embodiments, the locus comprises a sequence that is less methylated in diseased cells than in non-diseased cells.
In some embodiments, the methods further comprise adding sequence tags onto the ends of a population of nucleic acids before dividing the population of nucleic acids into equal portions, and step (c) comprises quantifying the remaining intact methylated copies of the locus in the first portion with primers that initiate amplification from the sequence tags; and step (e) comprises quantifying the remaining unmethylated intact copies of the locus in the second portion with primers that initiate amplification from the sequence tags.
These and other embodiments of the invention are further illustrated by the detailed description that follows.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 illustrates how the methods of the invention can be used to determine methylation at a locus.
FIG. 2 illustrates results of amplification of DNA at different methylated:unmethylated dilutions.
FIG. 3 illustrates the ability of McrBC to distinguish between DNA at different methylated:unmethylated dilutions. The arrows at the bottom of the figure indicate the approximate ΔCt between HhaI-cut and HhaI/McrBC double cut samples.
FIG. 4 illustrates analysis of DNA at a 1:2000 methylated:unmethylated dilution.
FIG. 5 illustrates a plot of change in cycle threshold as a function of dilution of methylated/unmethylated DNA.
FIG. 6 illustrates results from different methylated:unmethylated dilutions.
FIG. 7 illustrates a hypothetical methylation density progression in the development of disease.
FIG. 8 illustrates McrBC DNA restriction.
FIG. 9 illustrates amplification results from different McrBC dilutions restricting sparsely-methylated DNA.
FIG. 10 illustrates amplification results from different McrBC dilutions restricting densely-methylated DNA.
FIG. 11 illustrates using different restriction enzyme dilutions to determine optimum resolution between DNA with different methylation densities.
FIG. 12 illustrates what data is obtained when the methylation state of only particular nucleotides is detected in a hypothetical disease progression.
FIG. 13 illustrates what data is obtained when the average methylation density of a locus is detected in a hypothetical disease progression.
FIG. 14 depicts a portion of the p16 promoter (SEQ ID NO:1) methylated in vitro with M.Sss I.
FIG. 15 illustrates data demonstrating that methylation-dependent (i.e., McrBC) and methylation-sensitive (i.e., Aci I) restriction enzymes distinguish different methylation densities at a DNA locus.
FIG. 16 illustrates cycle threshold data demonstrating that methylation-dependent (i.e., McrBC) and methylation-sensitive (i.e., Aci I) restriction enzymes distinguish different methylation densities at a DNA locus.
FIG. 17 illustrates a consensus restriction map of kafirin genes. The relevant restriction sites are indicated vertically and the numbers indicate the distances scale in base-pairs. Each coding sequence is depicted as the blue-shaded arrow, and the region assayed is indicated by the black bar. The circles depict sites that are not present in every kafirin gene, and the color represents the number of genes that do not share the site. The orange circle (5′ most HhaI site) is conserved in 9 of 11 Kafirin genes, and the red circle (3′ most PstI site) is present in 10 of the 11.
FIG. 18 illustrates the heterogenous CG methylation and homogenous CNG methylation of eleven kafirin genes.



DETAILED DESCRIPTION OF THE INVENTION
I. Introduction
The present invention provides methods of detecting the presence of methylation at a locus within a population of nucleic acids using methylation-sensitive restriction enzymes, methylation-dependent restriction enzymes, and/or methylation-insensitive enzymes. According to the methods of the invention, nucleic acids comprising the locus of interest are cut with one or more restriction enzymes as described herein to generate populations of intact methylated loci, intact unmethylated loci, and/or intact hemimethylated loci. The loci are amplified, and the amplification products are compared. Comparison of the amplification products provides information regarding methylation at the locus.
DNA methylation plays important roles in gene regulation and therefore it is desirable to evaluate genomic methylation for numerous purposes. For example, the presence or absence of methylation at a particular locus can provide diagnostic and prognostic information regarding diseases associated with aberrant methylation at the locus.
II. Definitions
“Methylation” refers to cytosine methylation at C5 or N4 positions of cytosine (“5mC” and “4mC,” respectively), at the N6 position of adenine (“6mA”), or other types of nucleic acid methylation. Aberrant methylation of a DNA sequence (i.e., hypermethylation or hypomethylation) may be associated with a disease, condition or phenotype (e.g., cancer, vascular disease, cognitive disorders, or other epigenetic trait). An “unmethylated” DNA sequence contains substantially no methylated residues at least at recognition sequences for a particular methylation-dependent or methylation-sensitive restriction enzyme used to evaluate the DNA. “Methylated” DNA contains methylated residues at least at the recognition sequences for a particular methylation-dependent or methylation-sensitive restriction enzyme used to evaluate the DNA. It is understood that while a DNA sequence referred to as “unmethylated” may generally have substantially no methylated nucleotides along its entire length, the definition encompasses nucleic acid sequences that have methylated nucleotides at positions other than the recognition sequences for restriction enzymes. Likewise, it is understood that while a DNA sequence referred to as “methylated” may generally have methylated nucleotides along its entire length, the definition encompasses nucleic acid sequences that have unmethylated nucleotides at positions other than the recognition sequences for restriction enzymes. “Hemimethylated” DNA refers to double stranded DNA in which one strand of DNA is methylated at a particular locus and the other strand is unmethylated at that particular locus.
A “methylation-dependent restriction enzyme” refers to a restriction enzyme that cleaves at or near a methylated recognition sequence, but does not cleave at or near the same sequence when the recognition sequence is methylated. Methylation-dependent restriction enzymes include those that cut at a methylated recognition sequence (e.g., DpnI) and enzymes that cut at a sequence that is at the recognition sequence (e.g., McrBC). For example, McrBC require two half-sites. Each half-site must be a purine followed by 5-methyl-cytosine (R5mC) and the two half-sites must be no closer than 20 base pairs and no farther than 4000 base pairs away from each other (N20-4000). McrBC generally cuts close to one half-site or the other, but cleavage positions are typically distributed over several base pairs approximately 32 base pairs from the methylated base. Exemplary methylation-dependent restriction enzymes include, e.g., McrBC (see, e.g., U.S. Pat. No. 5,405,760), McrA, MrrA, and Dpn I. One of skill in the art will appreciate that homologs and orthologs Of the restriction enzymes described herein are also suitable for use in the present invention.
A “methylation-sensitive restriction enzyme” refers to a restriction enzyme (e.g., PstI) that cleaves at or in proximity to an unmethylated recognition sequence but does not cleave at or in proximity to the same sequence when the recognition sequence is methylated. Exemplary methylation sensitive restriction enzymes are described in, e.g., McClelland et al, Nucleic Acids Res. 22(17):3640-59 (1994) and //rebase.neb.com. Suitable methylation-sensitive restriction enzymes that do not cleave at or near their recognition sequence when a cytosine within the recognition sequence is methylated at position C5 include, e.g., Aat II, Aci I, Ad I, Age I, Alu I, Asc I, Ase I, AsiS I, Bbe I, BsaA I, BsaH I, BsiE I, BsiW I, BsrF I, BssH II, BssK I, BstB I, BstN I, BstU I, Cla I, Eae I, Eag I, Fau I, Fse I, Hha I, HinP1 I, HinC II, Hpa II, Hpy99 I, HpyCH4 IV, Kas I, Mbo I, Mlu I, MapA1 I, Msp I, Nae I, Nar I, Not I, Pml I, Pst I, Pvu I, Rsr II, Sac II, Sap I, Sau3A I, Sfl I, Sfo I, SgrA I, Sma I, SnaB I, Tsc I, Xma I, and Zra I. Suitable methylation-sensitive restriction enzymes that do not cleave at or near their recognition sequence when an adenosine within the recognition sequence is methylated at position N6 include, e.g., Mbo I. One of skill in the art will appreciate that homologs and orthologs of the restriction enzymes described herein are also suitable for use in the present invention. One of skill in the art will further appreciate that a methylation-sensitive restriction enzyme that fails to cut in the presence of methylation of a cytosine at or near its recognition sequence, may be insensitive to the presence of methylation of an adenosine at or near its recognition sequence. Likewise, a methylation-sensitive restriction enzyme that fails to cut in the presence of methylation of an adenosine at or near its recognition sequence, may be insensitive to the presence of methylation of a cytosine at or near its recognition sequence. For example, Sau3AI is sensitive (i.e., fails to cut) to the presence of a methylated cytosine at or near its recognition sequence, but is insensitive (i.e., cuts) to the presence of a methylated adenosine at or near its recognition sequence.
A “methylation insensitive restriction enzyme” refers to a restriction enzyme that cuts DNA regardless of the methylation state of the base of interest (A or C) at or near the recognition sequence of the enzyme. One of skill in the art will appreciate that a methylation-insensitive restriction enzyme that cuts in the presence of methylation of an adenosine at or near its recognition sequence, may be sensitive to the presence of methylation of a cytosine at or near its recognition sequence, i.e., will fail to cut. Likewise, a methylation-insensitive restriction enzyme that cuts in the presence of methylation of a cytosine at or near its recognition sequence, may be sensitive to the presence of methylation of an adenosine at or near its recognition sequence. For example, Sau3AI is insensitive (i.e., cuts) to the presence of a methylated adenosine at or near its recognition sequence, but is sensitive (i.e., fails to cut) to the presence of a methylated cytosine at or near its recognition sequence.
“Isoschizomers” refer to distinct restriction enzymes have the same recognition sequence. As used in this definition, the “same recognition sequence” is not intended to differentiate between methylated and unmethylated sequences. Thus, an “isoschizomeric partner” of a methylation-dependent or methylation-sensitive restriction enzyme is a restriction enzyme that recognizes the same recognition sequence as the methylation-dependent or methylation-sensitive restriction enzyme regardless of whether a nucleotide in the recognition sequence is methylated.
As used herein, a “recognition sequence” refers to a primary nucleic acid sequence and does not reflect the methylation status of the sequence.
The “methylation density” refers to the number of methylated residues in a given locus of DNA divided by the total number of nucleotides in the same DNA sequence that are capable of being methylated. Methylation density is determined for cytosines only or adenosines only.
“Dividing” or “divided” in the context of dividing DNA, typically refers to dividing a population of nucleic acids isolated from a sample into two or more physically distinct portions, each of which comprise all of the sequences present in the sample. In some cases, “dividing” or “divided” refers to dividing a population of nucleic acids isolated from a sample into two or more physically distinct parts that do not contain all of the sequences present in the sample.
Cleaving DNA “under conditions that allow for at least some copies of potential restriction enzyme cleavage sites in the locus to remain uncleaved” refers to any combination of reaction conditions, restriction enzyme and enzyme concentration and/or DNA resulting in at least some of the DNA comprising a potential restriction enzyme cleavage site to remain uncut. For example, a partial digestion of the DNA (e.g., by limiting the amount of enzyme or the amount of time of the digestion) allows some potential restriction enzyme cleavage sites in the locus to remain uncut. Alternatively, a complete digestion using a restriction enzyme such as McrBC will result in some potential restriction enzyme cleavage sites in the locus to remain uncut because the enzyme does not always cut between the two recognition half sites, thereby leaving at least some uncleaved copies of a locus in a population of sequences wherein the locus is defined by the two recognition half-sites. A “potential restriction enzyme cleavage site” refers to a sequence that a restriction enzyme is capable of cleaving (i.e., comprising the appropriate nucleotide sequence and methylation status) when it recognizes the enzymes recognition sequence, which may be the same or different from the cleavage site.
A “partial digestion” of DNA as used herein refers to contacting DNA with a restriction enzyme under appropriate reaction conditions such that the restriction enzyme cleaves some (e.g., less than about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%) but not all of possible cleavage sites for that particular restriction enzyme in the DNA. A partial digestion of the sequence can be achieved, e.g., by contacting DNA with an active restriction enzyme for a shorter period of time than is necessary to achieve a complete digestion and then terminating the reaction, by contacting DNA with less active restriction enzyme than is necessary to achieve complete digestion with a set time period (e.g., 30, 60, 90, 120, 150, 150, or 240 minutes), or under other altered reaction conditions that allow for the desired amount of partial digestion. “Possible sites” are generally enzyme recognition sequences, but also include situations where an enzyme cleaves at a sequence other than the recognition sequence (e.g., McrBC).
A “complete digestion” of DNA as used herein refers to contacting DNA with a restriction enzyme for sufficient time and under appropriate conditions to allow for cleavage of at least 95%, and typically at least 99%, or all of the restriction enzyme recognition sequences for the particular restriction enzyme. Conditions, including the time, buffers and other reagents necessary for complete digestions are typically provided by manufacturers of restriction enzymes. Those of skill in the art will recognize that the quality of the DNA sample may prevent complete digestion.
“An agent that modifies unmethylated cytosine” refers to any agent that alters the chemical composition of unmethylated cytosine but does not change the chemical composition of methylated cytosine. Examples of such agents include sodium bisulfite, sodium metabisulfite, permanganate, and hydrazine.
“Genomic DNA” as used herein refers to the entire genomic sequence, or a part thereof, of an individual. A “subset” of the genomic DNA refers to a part of the entire genomic sequence, i.e., a subset contains only some, but not all of the loci of an entire genome. The individual may be an animal, a plant, a fungus, or a prokaryote, as well as a cell, tissue, organ, or other part of an organism.
A “methylation profile” refers to a set of data representing the methylation state of DNA from e.g., the genome of an individual or cells and tissues of an individual. The profile can indicate the methylation state of every base pair in an individual or can comprise information regarding a subset of the base pairs (e.g., the methylation state of specific restriction enzyme recognition sequence) in a genome.
“Amplifying” DNA refers to any chemical, including enzymatic, reaction that results in an increased number of copies of a template nucleic acid sequence or an increased signal indicating that the template nucleic acid is present in the sample. Amplification reactions include polymerase chain reaction (PCR) and ligase chain reaction (LCR) (see U.S. Pat. Nos. 4,683,195 and 4,683,202; PCR PROTOCOLS: A GUIDE TO METHODS AND APPLICATIONS (Innis et al., eds, 1990)), strand displacement amplification (SDA) (Walker, et al. Nucleic Acids Res. 20(7):1691-6 (1992); Walker PCR Methods Appl 3(1):1-6 (1993) transcription-mediated amplification (Phyffer, et al., J. Clin. Microbiol. 34:834-841 (1996); Vuorinen, et al., J. Clin. Microbiol. 33:1856-1859 (1995)), nucleic acid sequence-based amplification (NASBA) (Compton, Nature 350(6313):91-2 (1991), rolling circle amplification (RCA) (Lisby, Mol. Biotechnol. 12(1):75-99 (1999)); Hatch et al., Genet. Anal. 15(2):35-40 (1999)); branched DNA signal amplification (bDNA) (see, e.g., Iqbal et al., Mol. Cell Probes 13(4):315-320 (1999)), and linear amplification. Amplifying includes, e.g., ligating adaptors that comprise T3 or T7 promoter sites to the template nucleic acid sequence and using T3 or T7 polymerases to amplify the template nucleic acid sequence.
A “locus” as used herein refers to a target sequence within a population of nucleic acids (e.g., a genome). If a single copy of the target sequence is present in the genome, then “locus” will refer to a single locus. If multiple copies of the target sequence are present in the genome, then “locus” will refer to all loci that contain the target sequence in the genome.
III. Detecting Methylation at a Locus within a Nucleic Acid Population
Methods of the invention may comprise comparing the presence or absence or amounts of intact DNA following restriction of a sample divided into at least two portions, wherein the portions are treated with different restriction enzymes. In many embodiments, a first portion is contacted with a methylation-dependent restriction enzyme (producing intact unmethylated DNA and fragmented methylated DNA) and a second portion is contacted with a methylation-sensitive restriction enzyme (producing intact methylated DNA and fragmented unmethylated DNA). The intact copies of the locus from each portion are analyzed after the restriction digests and compared.
In some embodiments, a third portion of nucleic acids comprising the locus is not digested with a restriction enzyme to provide an analysis of the total number of intact copies of a locus in a sample. The total number of the intact copies of the locus can be compared to the number of methylated loci and/or the number of unmethylated loci to verify that the number of methylated loci and unmethylated loci are equal to the total number of loci.
In further embodiments, a fourth portion of nucleic acids comprising the locus is digested with both the methylation-sensitive restriction enzyme and the methylation-dependent restriction enzyme and any intact loci are quantified (e.g., quantitatively amplified or detected by hybrid capture). The total number of intact loci remaining after the double digestion can be compared to the number of methylated copies of the locus, unmethylated copies of the locus, and/or total copies of the locus to verify that the number of methylated copies and unmethylated copies are equal to the total number of copies and to verify that the cutting of the methylation sensitive and methylation dependent restriction enzymes is complete.
In even further embodiments, a fifth portion of nucleic acids comprising the locus is digested with a methylation-insensitive restriction enzyme (i.e., either insensitive to methylation of an adenosine or of a cytosine residue at its recognition sequence) and any intact copies of the locus are detected. The total number of intact copies remaining after digestion can be compared to the number of methylated copies, unmethylated copies, and/or total copies to verify that the cutting of the other methylation sensitive and methylation dependent restriction enzymes is complete; and/or to identify mutations in copies of the locus that affect the recognition site of the methylation sensitive and methylation dependent restriction enzymes.
Thus, a comparison of at least five separate amplified nucleic acid populations can be made:

    
    
        (1) an untreated or mock treated population where virtually all of the copies of the locus remain in tact;
        (2) a population treated with a methylation-dependent restriction enzyme where virtually all of the unmethylated copies of the locus remain intact;
        (3) a population treated with a methylation-sensitive restriction enzyme where virtually all of the methylated copies of the locus remain intact;
        (4) a population treated with both a methylation-dependent restriction enzyme and a methylation-sensitive restriction enzyme which contains no or few intact copies of the locus; and
        (5) a population treated with a methylation insensitive restriction enzyme (i.e., either insensitive to methylation at an adenosine or at a cytosine residue at or near its recognition sequence) which contains no or few intact copies of the locus, except copies of the locus that are mutated at the recognition site of the restriction enzyme.
    
    


Typically, the samples are divided into equal portions, each of which contains all of the sequences present in the sample. In some cases, the samples may be divided into parts that do not contain all of the sequences present in the sample. However, by comparing results from different combinations of restriction digests, the number of methylated and unmethylated copies of the locus of interest can be determined. Any of the above populations can thus be compared to any other population. For example, populations (1) and (2) can be compared with one another; or either population (1) or (2) can be compared with another population, e.g., population (4).
The order in which the digest(s) are performed are not critical. Thus, although it may be preferable to perform a digest in a certain order, e.g., to first digest with a particular class of methylation-sensing enzymes, e.g., methylation-sensitive enzymes, it is not necessary. Similarly, it may be preferable to perform a double digest.
In some embodiments, the nucleic acid may be obtained from a sample comprising a mixed population of members having different methylation profiles. For example, a biological sample may comprise at least one cell type with little or no methylation at a locus of interest and at least one cell type that is methylated at the locus. The proportion of the population constituting methylated or unmethylated loci can be assessed by determining the amount of undigested loci in a single-digested aliquot treated with only methylation-sensitive or methylation-dependent restriction enzyme(s) to the amount of undigested DNA in an aliquot treated with both methylation-sensitive and methylation-dependent restriction enzymes. As used in this context, a “single” digest may, in practice, be performed using more than one enzyme that is methylation-sensitive, or more than one enzyme that is methylation-dependent, whether used sequentially or simultaneously. For example, an aliquot that is digested with more than one methylation-sensitive restriction enzyme, but no methylation-dependent restriction enzymes is considered a “single” digest. A “double” digest is considered to be an aliquot that has been treated using both methylation-sensitive and methylation-dependent restriction enzymes, whether used sequentially or simultaneously, regardless of the number of methylation-sensitive and methylation-dependent restriction enzymes employed.
The amount of undigested DNA in the single digest relative to the double digest and the total number of copies of the locus in the sample is indicative of the proportion of cells that contain unmethylated vs methylated DNA at the locus of interest. Furthermore, such an analysis can serve as a control for the efficacy of the single digest, e.g. the presence of a detectable change in the amount of undigested DNA in the double digest compared to the amount in the single digest with a methylation-sensitive restriction enzyme is an indication that the single digest went to completion.
One of skill in the art will appreciate that, by selecting appropriate combinations of restriction enzymes (e.g., methylation-sensitive, methylation-dependent, and methylation-insensitive restriction enzymes), the methods of the invention can be used to determine cytosine methylation or adenosine methylation at a particular locus based on, e.g., the recognition sequence of the restriction enzyme. For example, by cutting a first portion of nucleic acids comprising a locus of interest with a methylation-sensitive restriction enzyme which fails to cut when a methylated cytosine residue is in its recognition sequence (e.g., Hha I), and cutting a second portion of nucleic acids comprising a locus of interest with a methylation-dependent restriction enzyme which cuts only if its recognition sequence comprises a methylated cytosine (e.g., McrBC), the cytosine methylation of a particular locus may be determined. Likewise, by cutting a first portion of nucleic acids comprising a locus of interest with a methylation-sensitive restriction enzyme which fails to cut when an adenosine residue is methylated in its recognition sequence (e.g., Mbo I), and cutting a second portion of nucleic acids comprising a locus of interest with a methylation-dependent restriction enzyme which cuts in the presence of methylated adenosines in its recognition sequence (e.g., Dpn I), the adenosine methylation of a particular locus may be determined. In some embodiments, all four sets of digestions are conducted in parallel for both adenosine methylation and cytosine methylation to simultaneously determine the adenosine methylation and the cytosine methylation of a particular locus.
In addition, restriction enzymes that are either sensitive to methylated cytosine or to methylated adenosine can be used in the methods of the invention to provide populations of cytosine methylated loci and adenosine methylated loci for comparison.
Suitable methylation-dependent restriction enzymes include, e.g., McrBC, McrA, MrrA, and DpnI. Suitable methylation-sensitive restriction enzymes include restriction enzymes that do not cut when a cytosine within the recognition sequence is methylated at position C5 such as, e.g., Aat II, Aci I, Acl I, Age I, Alu I, Asc I, Ase I, AsiS I, Bbe I, BsaA I, BsaH I, BsiE I, BsiW L, BsrF I, BssH II, BssK I, BstB I, BstN I, BstU I, Cla I, Eae I, Eag I, Fau I, Fse I, Hha I, HinP1 I, HinC II, Hpa II, Hpy99 I, HpyCH4 IV, Kas I, Mlu I, MapA1 I, Msp I, Nae I, Nar I, Not I, Pml I, Pst I, Pvu I, Rsr II, Sac II, Sap I, Sau3A I, Sfl I, Sfo I, SgrA I, Sma I, SnaB I, Tsc I, Xma I, and Zra I. Suitable methylation-sensitive restriction enzymes include restriction enzymes that do not cut when an adenosine within the recognition sequence is methylated at position N6 such as, e.g., Mbo I. One of skill in the art will appreciate that homologs and orthologs of the restriction enzymes described herein are also suitable for use in the present invention.
In some embodiments, the nucleic acid portions are treated with an agent that modifies a particular unmethylated base, such as sodium bisulfite, prior to treatment with restriction enzymes. The nucleic acids can then be treated and amplified using at least one primer that distinguishes between protected methylated and modified unmethylated nucleotides. The amplified portions are then compared to determine relative methylation. Certain quantitative amplification technologies employ one or more detection probes that are distinct from the amplification primers. These detection probes can also be designed to discriminate between protected methylated and modified unmethylated DNA.
This invention relies on routine techniques in the field of recombinant genetics. For example, methods of isolating genomic DNA, digesting DNA with restriction enzymes, ligating oligonucleotide sequences, detecting amplified and unamplified DNA, and sequencing nucleic acids are well known in the art. Basic texts disclosing the general methods of use in this invention include Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL (3rd ed. 2001); Kriegler, GENE TRANSFER AND EXPRESSION: A LABORATORY MANUAL (1990); and CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (Ausubel et al., eds., 2001)).
A. Digestion with Restriction Enzymes
Either partial or complete restriction enzyme digestions, depending on the restriction enzyme, can be used to provide information regarding the methylation density within a particular DNA locus. The restriction enzymes for use in the invention are typically selected based on a sequence analysis of the locus of interest. One or more enzymes in each category (e.g., methylation-dependent or methylation-sensitive) are then selected. The sequence analysis can be performed based on evaluating databases of known sequences or in some instances, can be based on empirical determinations, e.g., to take into account variants such as mutations, that may be present in a particular subject.
1. DNA Samples
DNA can be obtained from any biological sample can be used, e.g., from cells, tissues, and/or fluids from an organism (e.g., an animal, plant, fungus, prokaryote). The samples may be fresh, frozen, preserved in fixative (e.g., alcohol, formaldehyde, paraffin, or PreServeCyteTM) or diluted in a buffer. Biological samples include, e.g., skin, blood or a fraction thereof, tissues, biopsies (from e.g., lung, colon, breast, prostate, cervix, liver, kidney, brain, stomach, esophagus, uterus, testicle, skin, bone, kidney, heart, gall bladder, bladder, and the like), body fluids and secretions (e.g., blood, urine, mucus, sputum, saliva, cervical smear specimens, marrow, feces, sweat, condensed breath, and the like). Biological samples also include, leaves, stems, roots, seeds, petals, pollen, spore, mushroom caps, and sap.
2. Complete Digestion
When a DNA sample comprising a locus of interest is completely digested with a methylation sensing restriction enzyme (i.e., a methylation-dependent or methylation sensitive restriction enzyme), the information provided includes the presence or absence of methylation at recognition sequences of the restriction enzyme. The presence of intact DNA in a locus comprising the cut site of the restriction enzyme indicates that the appropriate methylation state of the recognition site necessary for cleavage by the methylation-sensitive or methylation-dependent restriction enzyme was not present at or near the locus.
The amount of intact DNA can be compared to a control representing an equal amount of DNA from the sample that was not contacted with the restriction enzyme. Alternatively, the amount of intact DNA at a locus can be compared to a second locus or to the same locus in DNA isolated from another cell. In another alternative, the amount of intact DNA at a locus can be compared to DNA having a known or expected number of methylated and monitorable restriction sites. In some embodiments, the DNA being compared is approximately the same size. Those of skill in the art will appreciate that other controls are also possible. Thus, by detecting the amount of intact DNA at the locus following restriction enzyme digestion, the relative number of methylated alleles is determined.
Use of restriction enzymes that have a variable cleavage pattern near the recognition sequence (e.g., McrBC) provides a special case for complete digestions of DNA. In this case, even if the locus contains a recognition sequence in the appropriate methylation state, some of the fragments containing a methylated locus will remain intact because cleavage of the DNA will occur outside the locus according to a function of probability. Therefore, a complete digestion with McrBC behaves similarly to a partial digestion with a methylation sensitive restriction enzyme (which cuts at its recognition site) with respect to the number of intact alleles.
The mechanism of McrBC DNA cutting occurs as follows. An eight subunit complex of McrB binds to each of two recognition half sites (purine-methylC represented as (A or G)mC). See FIG. 8. These complexes then recruit one McrC subunit to their respective half sites and start to translocate along the DNA mediated by GTP hydrolysis. When two McrBC bound complexes contact each other, a double-complex is formed and restriction occurs. Cutting will generally not occur if the two half sites are closer than 20 bp and restriction resulting from half sites as far as 4 kb from one another have been observed, though are rare. Restriction may occur  ̃32 bp to the left or right of either bound half site, giving four possible cut site locations:  ̃32 bp 5′ of the first half site,  ̃32 bp 3′ of the first half site,  ̃32 bp 5′ of the second half site, and  ̃32 bp 3′ of the second half site. Therefore, it is possible for two half sites to exist within a locus defined by PCR primers and for cleavage to occur outside of the locus. It is also possible for two half sites to exist outside of the locus and for a cut to occur within the locus. It is also possible for one site to exist in the locus and for another to exist outside of the locus and for a cut to occur either within or outside of the locus. Thus, the more methylated half sites that are “in the vicinity” of the locus (whether literally between the amplification primers or in neighboring flanking sequence), the more likely a cut will be observed within the locus for a given concentration of McrBC. Accordingly, the number of copies of a methylated locus that are cleaved by McrBC in a complete or partial digestion will be proportional to the density of methylated nucleotides.
3. Partial Digestions
The amount of cleavage with a methylation sensitive or methylation-dependent restriction enzyme in a partial (i.e., incomplete) digestion, reflects not only the number of fragments that contain any DNA methylation at a locus, but also the average methylation density within the locus of DNA in the sample. For instance, when DNA fragments containing the locus have a higher methylation density, then a partial digestion using a methylation-dependent restriction enzyme will cleave these fragments more frequently within the locus. Similarly, when DNA fragments containing the locus have a lower methylation density, then a partial digestion using a methylation-dependent restriction enzyme will cleave these fragments less frequently within the locus, because fewer recognition sites are present. Alternatively, when a methylation sensitive restriction enzyme is used, DNA fragments with a higher methylated density are cleaved less, and thus more intact DNA strands containing the locus are present. In each of these cases, the digestion of DNA sample in question is compared to a control value such as those discussed above for complete digestions.
In some embodiments, the DNA sample can be split into equal portions, wherein each portion is submitted to a different amount of partial digestion with McrBC or another methylation-dependent restriction enzyme. The amount of intact locus in the various portions (e.g., as measured by quantitative DNA amplification) can be compared to a control population (either from the same sample representing uncut DNA or equivalent portions from another DNA sample). In cases where the equivalent portions are from a second DNA sample, the second sample can have an expected or known number of methylated nucleotides (or at least methylated restriction enzyme recognition sequences) or, alternatively, the number of methylated recognition sequences can be unknown. In the latter case, the control sample will often be from a sample of biological relevance, e.g., from a diseased or normal tissue, etc.
In some embodiments, the DNA sample is partially digested with one or more methylation-sensitive restriction enzymes and then amplified to identify intact loci. Controls in these cases are similar to those used for methylation-dependent restriction enzyme digestions described above. Untreated controls are undigested, and any treated control DNA samples are digested with methylation-sensitive restriction enzymes.
It can be useful to test a variety of conditions (e.g., time of restriction, enzyme concentration, different buffers or other conditions that affect restriction) to identify the optimum set of conditions to resolve subtle or gross differences in methylation density among two or more samples. The conditions may be determined for each sample analyzed or may be determined initially and then the same conditions may be applied to a number of different samples.
4. Generation of Control Values
Control values can represent either external values (e.g., the number of intact loci in a second DNA sample with a known or expected number of methylated nucleotides or methylated restriction enzyme recognition sequences) or internal values (e.g., a second locus in the same DNA sample or the same locus in a second DNA sample). While helpful, it is not necessary to know how many nucleotides (i.e. the absolute value) in the control are methylated. For example, for loci in which methylation results in a disease state, knowledge that the locus is more methylated than it is in normal cells can indicate that the subject from which the sample was obtained may have the disease or be in the early stages of developing disease.
In cases where the same DNA sample includes a control locus, multiplex amplification, e.g., multiplex PCR, can be used to analyze two more loci (e.g., at least one target locus and at least one control locus).
DNA samples can vary by two parameters with respect to methylation: (i) the percentage of total copies in a population that have any methylation at a specific locus, and (ii) for copies with any DNA methylation, the average methylation density among the copies. It is ideal, though not required, to use control DNAs that evaluate both of these parameters in a test sample.
Control DNAs with known methylated cytosines are produced using any number of DNA methylases, each of which can have a different target methylation recognition sequence. This procedure can create a population of DNA fragments that vary with respect to the methylation density (i.e., the number of methylated cytosines per allele). Partial methylase reactions can also be used, e.g., to produce a normally distributed population with a mode at the average methylation density for the population. In some embodiments, the mode can be adjusted for a given population as a function of the completeness of the methylase reaction. Control DNAs can also be synthesized with methylated and unmethylated DNA bases.
In some cases, a DNA target with a known sequence is used. A desired control DNA can be produced by selecting the best combination of methylases and restriction enzymes for the analysis. First, a map of sites that can be methylated by each available methylase is generated. Second, a restriction map of the locus is also produced. Third, methylases are selected and are used to in vitro methylate the control DNA sample to bring about a desired methylation pattern, which is designed to perform optimally in combination with the restriction enzymes used in the methylation analysis of the test DNA and control DNA samples. For example, M.HhaI methylates the site (G*CGC) and McrBC recognizes two half sites with the motif (RpC). Therefore, each methylated M.HhaI site in the control sequence is recognized by McrBC.
Similarly, a population of molecules may be then treated with a DNA methylase (e.g., M.SssI) in the presence of magnesium to result in a desired methylation density. If the reaction is allowed to run to completion, nearly all of the sites that can be methylated will be methylated, resulting in a high and homogeneous methylation density. If the reaction is limited in its course, a lower average methylation density (or partial methylation) will result (i.e., all possible sites are not methylated due to timing of reaction and/or concentration of enzyme). In this way, the desired average methylation density of the control DNA can be produced. The methylated control DNA can be precisely characterized by determining the number of methylated cytosines through bisulfite sequencing. Alternatively, the methylation control DNA can be precisely characterized by determining the number of methylated cytosines through a comparison to other known control DNAs as described herein.
For more precise prediction of methylation densities, it may be useful to generate a control set of DNA that can conveniently serve as a standard curve where each sample in the control set has a different methylation density, either known or unknown. By cutting the multiple samples with a methylation-dependent restriction enzyme or a methylation-sensitive restriction enzyme under conditions that allow for at least some copies of potential restriction enzyme cleavage sites in the locus to remain uncleaved and subsequently amplifying the remaining intact copies of a locus, a standard curve of the amount of intact copies (e.g., represented by Ct values) can be generated, thereby correlating the amount of intact DNA to different methylation densities. The standard curve can then be used to determine the methylation density of a test DNA sample by interpolating the amount of intact DNA in the sample following restriction and amplification as described herein.
B. Calculation of Methylation Density Based on Cycle Thresholds
As described herein, cycle thresholds (Ct) are a useful measurement for determining the initial amount of DNA template in an amplification reaction. Accordingly, Ct values from samples treated with a methylation-dependent and/or methylation-sensitive restriction enzyme and amplified as described herein can be used to calculate methylation density. A change in Ct value between one sample and a control value (which can represent the Ct value from a second sample) is predictive of relative methylation density. Because amplification in PCR theoretically doubles copies every cycle, 2X is proportional to the number of copies in the amplification during exponential amplification, where X is the number of cycles. Thus 2Ct is proportional to the amount of intact DNA at the initiation of amplification. The change of Ct (ΔCt) between two samples or between a sample and a control value (e.g., representing a Ct value from a control) represents the difference in initial starting template in the samples. Therefore, 2|ΔCt| is proportional to the relative methylation density difference between a sample and a control or a second sample. For instance, a difference of 1.46 in the Ct between two samples (each treated with a methylation-dependent restriction enzyme and subsequently amplified) indicates that one sample has approximately 2.75 (i.e., 2(1.46)=2.75) times more methylated nucleotides within the monitored sites at a locus than the other sample.
C. Detecting DNA
The presence and quantity of DNA cleaved by the restriction enzymes can be detected using any means known in the art including, e.g., quantitative amplification, hybrid capture, or combinations thereof.
1. Quantitative Amplification
In some embodiments, the presence and quantity of DNA cleaved by the restriction enzymes can be determined by amplifying the locus following digestion. By using amplification techniques (e.g., the polymerase chain reaction (PCR)) that require the presence of an intact DNA strand for amplification, the presence and amount of remaining uncut DNA can be determined. For example, PCR reactions can be designed in which the amplification primers flank a particular locus of interest. Amplification occurs when the locus comprising the two primers remains intact following a restriction digestion. If the amount of total and intact DNA is known, the amount of cleaved DNA can be determined. Since cleavage of the DNA depends on the methylation state of the DNA, the intact and cleaved DNA represents different methylation states.
Amplification of a DNA locus using reactions is well known (see U.S. Pat. Nos. 4,683,195 and 4,683,202; PCR PROTOCOLS: A GUIDE TO METHODS AND APPLICATIONS (Innis et al., eds, 1990)). Typically, PCR is used to amplify DNA templates. However, alternative methods of amplification have been described and can also be employed, as long as the alternative methods amplify intact DNA to a greater extent than the methods amplify cleaved DNA.
DNA amplified by the methods of the invention can be further evaluated, detected, cloned, sequenced, and the like, either in solution or after binding to a solid support, by any method usually applied to the detection of a specific DNA sequence such as PCR, oligomer restriction (Saiki, et al., Bio/Technology 3:1008-1012 (1985)), allele-specific oligonucleotide (ASO) probe analysis (Conner, et al., PNAS USA 80:278 (1983)), oligonucleotide ligation assays (OLAs) (Landegren, et al., Science 241:1077, (1988)), and the like. Molecular techniques for DNA analysis have been reviewed (Landegren, et al., Science 242:229-237 (1988)).
Quantitative amplification methods (e.g., quantitative PCR or quantitative linear amplification) can be used to quantify the amount of intact DNA within a locus flanked by amplification primers following restriction digestion. Methods of quantitative amplification are disclosed in, e.g., U.S. Pat. Nos. 6,180,349; 6,033,854; and 5,972,602, as well as in, e.g., Gibson et al., Genome Research 6:995-1001 (1996); DeGraves, et al., Biotechniques 34(1):106-10, 112-5 (2003); Deiman B, et al., Mol Biotechnol. 20(2):163-79 (2002). Amplifications may be monitored in “real time.”
In general, quantitative amplification is based on the monitoring of the signal (e.g., fluorescence of a probe) representing copies of the template in cycles of an amplification (e.g., PCR) reaction. In the initial cycles of the PCR, a very low signal is observed because the quantity of the amplicon formed does not support a measurable signal output from the assay. After the initial cycles, as the amount of formed amplicon increases, the signal intensity increases to a measurable level and reaches a plateau in later cycles when the PCR enters into a non-logarithmic phase. Through a plot of the signal intensity versus the cycle number, the specific cycle at which a measurable signal is obtained from the PCR reaction can be deduced and used to back-calculate the quantity of the target before the start of the PCR. The number of the specific cycles that is determined by this method is typically referred to as the cycle threshold (Ct). Exemplary methods are described in, e.g., Heid et al. Genome Methods 6:986-94 (1996) with reference to hydrolysis probes.
One method for detection of amplification products is the 5′-3′ exonuclease “hydrolysis” PCR assay (also referred to as the TaqManTM assay) (U.S. Pat. Nos. 5,210,015 and 5,487,972; Holland et al., PNAS USA 88: 7276-7280 (1991); Lee et al., Nucleic Acids Res. 21: 3761-3766 (1993)). This assay detects the accumulation of a specific PCR product by hybridization and cleavage of a doubly labeled fluorogenic probe (the “TaqManTM” probe) during the amplification reaction. The fluorogenic probe consists of an oligonucleotide labeled with both a fluorescent reporter dye and a quencher dye. During PCR, this probe is cleaved by the 5′-exonuclease activity of DNA polymerase if, and only if, it hybridizes to the segment being amplified. Cleavage of the probe generates an increase in the fluorescence intensity of the reporter dye.
Another method of detecting amplification products that relies on the use of energy transfer is the “beacon probe” method described by Tyagi and Kramer, Nature Biotech. 14:303-309 (1996), which is also the subject of U.S. Pat. Nos. 5,119,801 and 5,312,728. This method employs oligonucleotide hybridization probes that can form hairpin structures. On one end of the hybridization probe (either the 5′ or 3′ end), there is a donor fluorophore, and on the other end, an acceptor moiety. In the case of the Tyagi and Kramer method, this acceptor moiety is a quencher, that is, the acceptor absorbs energy released by the donor, but then does not itself fluoresce. Thus, when the beacon is in the open conformation, the fluorescence of the donor fluorophore is detectable, whereas when the beacon is in hairpin (closed) conformation, the fluorescence of the donor fluorophore is quenched. When employed in PCR, the molecular beacon probe, which hybridizes to one of the strands of the PCR product, is in the open conformation and fluorescence is detected, while those that remain unhybridized will not fluoresce (Tyagi and Kramer, Nature Biotechnol. 14: 303-306 (1996)). As a result, the amount of fluorescence will increase as the amount of PCR product increases, and thus may be used as a measure of the progress of the PCR. Those of skill in the art will recognize that other methods of quantitative amplification are also available.
Various other techniques for performing quantitative amplification of a nucleic acids are also known. For example, some methodologies employ one or more probe oligonucleotides that are structured such that a change in fluorescence is generated when the oligonucleotide(s) is hybridized to a target nucleic acid. For example, one such method involves is a dual fluorophore approach that exploits fluorescence resonance energy transfer (FRET), e.g., LightCyclerTM hybridization probes, where two oligo probes anneal to the amplicon. The oligonucleotides are designed to hybridize in a head-to-tail orientation with the fluorophores separated at a distance that is compatible with efficient energy transfer. Other examples of labeled oligonucleotides that are structured to emit a signal when bound to a nucleic acid or incorporated into an extension product include: ScorpionsTM probes (e.g., Whitcombe et al., Nature Biotechnology 17:804-807, 1999, and U.S. Pat. No. 6,326,145), SunriseTM (or AmplifluorTM) probes (e.g., Nazarenko et al., Nuc. Acids Res. 25:2516-2521, 1997, and U.S. Pat. No. 6,117,635), and probes that form a secondary structure that results in reduced signal without a quencher and that emits increased signal when hybridized to a target (e.g., Lux probesTM).
In other embodiments, intercalating agents that produce a signal when intercalated in double stranded DNA may be used. Exemplary agents include SYBR GREENTM and SYBR GOLDTM. Since these agents are not template-specific, it is assumed that the signal is generated based on template-specific amplification. This can be confirmed by monitoring signal as a function of temperature because melting point of template sequences will generally be much higher than, for example, primer-dimers, etc.
2. Methylation State-Specific Amplification
In some embodiments, methylation-specific PCR can be employed to monitor the methylation state of specific nucleotides in a DNA locus. In these embodiments, following or preceding digestion with the restriction enzyme, the DNA is combined with an agent that modifies unmethylated cytosines. For example, sodium bisulfite is added to the DNA, thereby converting unmethylated cytosines to uracil, leaving the methylated cytosines intact. One or more primers are designed to distinguish between the methylated and unmethylated sequences that have been treated with sodium bisulfite. For example, primers complementary to the bisulfite-treated methylated sequence will contain guanosines, which are complementary to endogenous cytosines. Primers complementary to the bisulfite-treated unmethylated sequence will contain adenosine, which are complementary to the uracil, the conversion product of unmethylated cytosine. Preferably, nucleotides that distinguish between the converted methylated and unmethylated sequences will be at or near the 3′ end of the primers. Variations of methods using sodium bisulfite-based PCR are described in, e.g., Herman et al., PNAS USA 93:9821-9826 (1996); U.S. Pat. Nos. 5,786,146 and 6,200,756.
3. Hybrid Capture
In some embodiments, nucleic acid hybrid capture assays can be used to detect the presence and quantity of DNA cleaved by the restriction enzymes. This method can be used with or without amplifying the DNA. Following the restriction digests, RNA probes which specifically hybridize to DNA sequences of interest are combined with the DNA to form RNA:DNA hybrids. Antibodies that bind to RNA:DNA hybrids are then used to detect the presence of the hybrids and therefore, the presence and amount of uncut DNA. DNA fragments that are restricted in a window of sequence that is complimentary to the RNA probe hybridize less efficiently to the RNA probe than do DNA fragments that remain in tact in the window of sequence being monitored. The amount of hybridization allows one to quantify intact DNA, and the quantity of DNA methylation can be inferred directly from the quantity of intact DNA from different restriction enzyme treatments (i.e., methylation-sensitive and/or methylation-dependent restriction enzyme treatments).
Methods of detecting RNA:DNA hybrids using antibodies are known in the art and are described in, e.g., Van Der Pol et al., J. Clin. Microbiol. 40(10): 3558 (2002); Federschneider et al., Am. J. Obstet. Gynecol. 191(3):757 (2004); Pretet et al., J. Clin. Virol. 31(2):140-7 (2004); Giovannelli et al., J. Clin. Microbiol. 42(8):3861 (2004); Masumoto et al., Gynecol. Oncol. 94(2):509-14 (2004); Nonogaki et al., Acta Cytol. 48(4):514 (2004); Negri et al., Am. J. Clin. Pathol. 122(1):90 (2004); Sarian et al., Gynecol. Oncol. 94(l):181 (2004); Oliveira et al., Diagn. Cytopathol. 31(1):19 (2004); Rowe et al., Diagn. Cytopathol. 30(6):426 (2004); Clavel et al., Br. J. Cancer 90(9):1803-8 (2004); Schiller et al., Am. J. Clin. Pathol. 121(4):537 (2004); Arbyn et al., J. Natl. Cancer Inst. 96(4):280 (2004); Syrjanen et al., J. Clin. Microbiol. February 2004;42(2):505 (2004); Lin et al., J. Clin. Microbiol. 42(1):366 (2004); Guyot et al., BMC Infect. Dis. 25;3(1):23 (2003); Kim et al., Gynecol. Oncol. 89(2):210-7 (2003); Negri et al., Am J Surg Pathol. 27(2):187 (2003); Vince et al., J. Clin. Virol. Suppl 3:S109 (2002); Poljak et al., J. Clin. Virol. Suppl 3:S89 (2002). In some cases, the antibodies are labeled with a detectable label (e.g., an enzymatic label, an isotope, or a fluorescent label) to facilitate detection. Alternatively, the antibody:nucleic acid complex may be further contacted with a secondary antibody labeled with a detectable label. For a review of suitable immunological and immunoassay procedures, see, e.g., Harlow & Lane, ANTIBODIES, A LABORATORY MANUAL, Cold Spring Harbor Publication, New York (1988); Basic and Clinical Immunology (Stites & Terr eds., 7th ed. 1991); U.S. Pat. Nos. 4,366,241; 4,376,110; 4,517,288; and 4,837,168); Methods in Cell Biology: Antibodies in Cell Biology, volume 37 (Asai, ed. 1993).
Monoclonal, polyclonal antibodies, or mixtures thereof may be used to bind the RNA:DNA hybrids. Detection of RNA:DNA hybrids using monoclonal antibodies is described in, e.g., U.S. Pat. Nos. 4,732,847 and 4,833,084. Detection of RNA:DNA hybrids using polyclonal antibodies is described in, e.g., U.S. Pat. No. 6,686,151. The polyclonal or monoclonal antibodies may be generated with specific binding properties. For example, monoclonal or polyclonal antibodies that specifically bind to shorter (e.g., less than 20 base pairs) or longer (e.g., more than 100 base pairs) RNA:DNA hybrids may be generated. In addition, monoclonal or polyclonal antibodies may be produced that are either more or less sensitive to mismatches within the RNA:DNA hybrid.
Methods of producing polyclonal and monoclonal antibodies that react specifically with RNA:DNA hybrids are known to those of skill in the art. For example, preparation of polyclonal and monoclonal antibodies by immunizing suitable laboratory animals (e.g., chickens, mice, rabbits, rats, goats, horses, and the like) with an appropriate immunogen (e.g., an RNA:DNA hybrid). Such methods are described in, e.g., Coligan, Current Protocols in Immunology (1991); Harlow & Lane, supra; Goding, Monoclonal Antibodies: Principles and Practice (2d ed. 1986); and Kohler & Milstein, Nature 256:495497 (1975).
Antibodies can also be recombinantly produced. Antibody preparation by selection of antibodies from libraries of nucleic acids encoding recombinant antibodies packaged in phage or similar vectors is described in, e.g., Huse et al., Science 246:1275-1281 (1989) and Ward et al., Nature 341:544-546 (1989). In addition, antibodies can be produced recombinantly using methods known in the art and described in, e.g., Sambrook et al., Molecular Cloning, A Laboratory Manual (2nd ed. 1989); Kriegler, Gene Transfer and Expression: A Laboratory Manual (1990); and Current Protocols in Molecular Biology (Ausubel et al., eds., 1994)).
D. Detection Of Methylation Density
In some embodiments, the methods of the invention can be used to determine the methylation density of a locus. Determination of methylation density is described, e.g., in U.S. Patent Application No. 60/513,426, filed Oct. 21, 2003.
The quantity of methylation of a locus of DNA can be determined by providing a sample of genomic DNA comprising the locus, cleaving the DNA with a restriction enzyme that is either methylation-sensitive or methylation-dependent, and then quantifying the amount of intact DNA or quantifying the amount of cut DNA at the DNA locus of interest.
The amount of intact or cut DNA will depend on the initial amount of genomic DNA containing the locus, the amount of methylation in the locus, and the number (i.e., the fraction) of nucleotides in the locus that are methylated in the genomic DNA. The amount of methylation in a DNA locus can be determined by comparing the quantity of intact or cut DNA to a control value representing the quantity of intact or cut DNA in a similarly-treated DNA sample. As discussed below, the control value can represent a known or predicted number of methylated nucleotides. Alternatively, the control value can represent the quantity of intact or cut DNA from the same locus in another (e.g., normal, non-diseased) cell or a second locus.
By using at least one methylation-sensitive or methylation-dependent restriction enzyme under conditions that allow for at least some copies of potential restriction enzyme cleavage sites in the locus to remain uncleaved and subsequently quantifying the remaining intact copies and comparing the quantity to a control, average methylation density of a locus may be determined. If the methylation-sensitive restriction enzyme is contacted to copies of a DNA locus under conditions that allow for at least some copies of potential restriction enzyme cleavage sites in the locus to remain uncleaved, then the remaining intact DNA will be directly proportional to the methylation density, and thus may be compared to a control to determine the relative methylation density of the locus in the sample. Similarly, if a methylation-dependent restriction enzyme is contacted to copies of a DNA locus under conditions that allow for at least some copies of potential restriction enzyme cleavage sites in the locus to remain uncleaved, then the remaining intact DNA will be inversely proportional to the methylation density, and thus may be compared to a control to determine the relative methylation density of the locus in the sample.
The average methylation density within a locus in a DNA sample is determined by digesting the DNA with a methylation-sensitive or methylation-dependent restriction enzyme and quantifying the relative amount of remaining intact DNA compared to a DNA sample comprising a known amount of methylated DNA. In these embodiments, partial digestions or complete digestions can be used. As described above for uniformly methylated DNA, use of partial digestions allows for the determination of the average methylation density of the locus.
E. Detection of Methylation Differences Between Samples and at Specific Loci
The methods of the invention can be used to detect differences in methylation between nucleic acid samples (e.g., DNA or genomic DNA) and/or at specific loci. In some embodiments, the methods can be used to analyze a sample of DNA where all copies of a genomic DNA locus have an identical methylation pattern. In some embodiments, the DNA sample is a mixture of DNA comprising alleles of a DNA locus in which some alleles are more methylated than others. In some embodiments, a DNA sample contains DNA from two or more different cell types, wherein each cell type has a different methylation density at a particular locus (e.g., a cell from a tissue suspected of being diseased and a cell from a non-diseased tissue sample). For example, at some loci, neoplastic cells have different methylation densities compared to normal cells. If a tissue, body fluid, or secretion contains DNA from both normal and neoplastic cells, the DNA sample from the tissue, body fluid, or secretion will comprise a heterogeneous mixture of differentially methylated alleles. In this case, at a given locus, one set of alleles within the DNA (e.g., those derived from neoplastic cells in the sample) will have a different methylation density than the other set of alleles (e.g., those derived from normal cells).
In cases where a particular phenotype or disease is to be detected, DNA samples should be prepared from a tissue of interest, or as appropriate, from blood. For example, DNA can be prepared from biopsy tissue to detect the methylation state of a particular locus associated with cancer. The nucleic acid-containing specimen used for detection of methylated loci (see, e.g., Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (1995 supplement)) may be from any source including brain, colon, urogenital, hematopoietic, thymus, testis, ovarian, uterine, prostate, breast, colon, lung and renal tissue and may be extracted by a variety of techniques such as that described by Ausubel et al., CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (1995) or Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL (3rd ed. 2001).
Detection and identification of loci of altered methylation (compared to normal cells) in DNA samples can indicate that at least some of the cells from which the sample was derived are diseased. Such diseases include but are not limited to, e.g., low grade astrocytoma, anaplastic astrocytoma, glioblastoma, medulloblastoma, colon cancer, liver cancer, lung cancer, renal cancer, leukemia (e.g., acute lymphocytic leukemia, chronic lymphocytic leukemia, acute myeloid leukemia, chronic myeloid leukemia), lymphoma, breast cancer, prostate cancer, cervical cancer, endometrial cancer, neuroblastoma, cancer of the oral cavity (e.g., tongue, mouth, pharynx), esophageal cancer, stomach cancer, cancer of the small intestine, rectal cancer, anal cancer, cancer of the anal canal and anorectum, cancer of the intrahepatic bile duct, gallbladder cancer, biliary cancer, pancreatic cancer, bone cancer, cancer of the joints, skin cancer (e.g., melanoma, non-epithelial cancer, basal cell carcinoma, squamous cell carcinoma), soft tissue cancers, uterine cancer, ovarian cancer, vulval cancer, vaginal cancer, urinary cancer, cancer of the ureter, cancer of the eye, head and neck cancer, non-Hodgkin lymphoma, Hodgkin lymphoma, multiple myeloma, brain cancer, cancer of the nervous system. Identification of altered methylation profiles is also useful for detection and diagnosis of loss of genomic imprinting, fragile X syndrome and X-chromosome inactivation.
Specific loci that are suitable for analysis using the methods of the invention are described in, e.g., Costello and Plass, J. Med. Genet. 38:285-303 (2001) and Jones and Baylin, Nature. Rev. 3:415-428 (2002) and are set forth in Table 1 below.







TABLE 1







Examples of Genes Exhibiting Hypermethylation in Cancer










Effect of loss of function in tumor



Gene
development
Tumor types





RB
Loss of cell-cycle control
Retinoblastoma


MLH1
Increased mutation rate, drug
Colon, ovarian, endometrial, gastric



resistance


BRCA1
Genomic instability
Breast, ovarian


E-CAD
Increased cell motility
Breast, gastric, lung, prostate, colon, leukemia


APC
Aberrant cell transduction
Breast, lung, colon, gastric, esophageal, pancreatic,




hepatocellular


p16
Loss of cell-cycle control
Most tumor types


VHL
Altered protein degradation
Clear-cell renal cell carcinoma


p73
Loss of cell-cycle control
Leukemia, lymphoma, ovarian


RASSF1A
Aberrant cell transduction
Lung, breast, ovarian, kidney, nasopharyngeal


p15
Loss of cell-cycle control
Leukemia, lymphoma, gastric, squamous cell




carcinoma, hepatocellular


GSTP1
Increased DNA damage
Prostate


DAPK
Reduced apoptosis
Lymphoma, lung


MGMT
Increased mutation rate
Colon, lung, brain, esophageal, gastric


P14ARF
Loss of cell cycle control
Melanoma, non-melanoma skin cancer, pancreatic,




breast, head and neck, lung, mesothelioma,




neurofibromatosis, colon, soft tissue sarcoma.,




bladder, Hodgkin's, Ewing's sarcoma, Wilm's tumor,




osteosarcoma, rhabdomyosarcoma


ATM
Defective DNA repair
Leukemia, lymphoma


CDKN2B
Loss of cell cycle control
Breast, ovarian, prostate


FHIT
Defective DNA repair
Lung, pancreas, stomach, kidney, cervix, breast


MSH2
Defective DNA repair
Colon


NF1/2
Loss of cell cycle control
Neurofibroma


PTCH
Loss of cell cycle control
Skin, basal and squamous cell carcinomas, brain


PTEN
Loss of cell cycle control
Breast, thyroid, skin, head and neck, endometrial


SMAD4
Loss of cell cycle control
Pancreas, colon


SMARCA3/B1
Loss of cell cycle control
Colon


STK11
Loss of cell cycle control
Melanoma, gastrointestinal


TIMP3
Disruption of cellular matrix
Uterus, breast, colon, brain, kidney


TP53
Loss of cell cycle control; reduced
Colon, prostate, breast, gall bladder, bile duct,



apoptosis


BCL2
Loss of cell cycle control; reduced
Lymphoma, breast



apoptosis


OBCAM
Loss of cell cycle control
Ovarian


GATA4
Transcriptional silencing of
Colorectal, gastric, ovary



downstream genes


GATA5
Transcriptional silencing of
Colorectal, gastric, ovary



downstream genes


HIC1
Loss of cell cycle control
Epithelium, lymphoma, sarcoma





Abbreviations:


APC, adenomatous polyposis coli;


BRCA1, breast cancer 1;


DAPK, death-associated protein kinase;


E-cad, epithelial cadherin;


GSTP1 glutathione S-transferase π1;


MLH1, MutL homologue 1,


MGMT, O(6)-methylguanine-DNA methyltransferase;


p15, p15INK4b;


p16, p16INK4;


p73, p73;


Rb, retinoblastoma;


RASSF1a, Ras association domain family 1A;


VHL, von Hippel-Lindau;


ATM, ataxia telangiectasia mutated;


CDKN2, cyclin dependent kinase inhibitor;


FHIT, fragile histidine triad;


MSH2, mutS homologue 2;


NF1⁄2, neurofibromin 1⁄2;


PTCH, patched homologue;


PTEN, phosphatase and tensin homologue;


SMAD4, mothers against decapentaplegic homologue 4;


SMARCA3/B1, SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 3/subfamily B, member 1;


STK11, serine/threonine kinase 11;


TIMP3, tissue inhibitor of metalloproteinase 3;


Bcl-2m B-call CLL/Lymphoma 2;


OBCAM, opoid-binding cell adhesion molecule;


GATA, globin transcription factor;


HIC1, hypermethylated in cancer.






In some embodiments, the methylation of sample from the same individual is determined over a period of time, e.g., days, weeks, months, or years. Determination of changes in methylation can be useful for providing diagnoses; prognoses; therapy selection; and monitoring progression for various diseases; and, in the case of cancer, tumor typing and staging. While the methods of the invention also provide for the detection of specific methylation events, the present methods are particularly notable because they are not limited by a prediction or expectation that the methylation state of a particular nucleotide is determinative of a phenotype. In cases where the density of methylation (rather than the presence or absence of a particular methylated nucleotide) modulates gene expression, and where the methylation density of a locus reflects disease progression along a continuum, the present methods are particularly helpful.
Amplification primers can be designed to amplify loci associated with a particular phenotype or disease.
If desired, multiplex DNA methods can be used to amplify multiple targets from the same sample. The additional targets can represent controls (e.g., from a locus of known methylation status) or additional loci associated with a phenotype or disease.
In some embodiments, the methods of the invention are used to identify new loci associated with a disease phenotype, such as cancer, or are used to validate such an association.
F. Exemplary Methods of Determining Relative Methylation at a Locus
As described above, a number of possibilities are available for determining the relative amount of methylation at a genetic locus of interest. For example, partial or complete digestions can be performed, methylation-sensitive or methylation-dependent restriction enzymes can be used, sodium bisulfite treatment can be employed, etc. Without intending to limit the invention to a particular series of steps, the following possibilities are further exemplified.
In some embodiments, a DNA sample is digested (partially or to completion) with McrBC or another methyl-dependent restriction enzyme and a locus is subsequently amplified using quantitative DNA amplification (e.g., PCR, rolling circle amplification, and other methods known to those skilled in the art). The resulting kinetic profiles of the amplification reactions are compared to those derived from a similarly treated control DNA sample. Kinetic profiles of amplification reactions can be obtained by numerous means known to those skilled in the art, which include fluorescence reaction monitoring of TaqManTM, Molecular BeaconsTM, SYBRGREENTM incorporation, ScorpionTM probes, LuxTM probes, and others.
In some embodiments, the DNA sample is split into equal portions and one portion is treated with the methylation-dependent restriction enzyme and the other is not. The two portions are amplified and compared to determine the relative amount of methylation at the locus.
In some embodiments, the DNA sample can be split into equal portions, wherein each portion is submitted to a different amount of partial digestion with McrBC or another methylation-dependent restriction enzyme. The amount of intact locus in the various portions (e.g., as measured by quantitative DNA amplification) can be compared to a control population (either from the same sample representing uncut DNA or equivalent portions from another DNA sample). In cases where the equivalent portions are from a second DNA sample, the second sample can have an expected or known number of methylated nucleotides (or at least methylated restriction enzyme recognition sequences) or, alternatively, the number of methylated recognition sequences can be unknown. In the latter case, the control sample will often be from a sample of biological relevance, e.g., from a diseased or normal tissue, etc.
In some embodiments, the DNA sample is partially digested with one or more methylation-sensitive restriction enzymes and then amplified to identify intact loci. Controls in these cases are similar to those used for methylation-dependent restriction enzyme digestions described above. Untreated controls are undigested, and any treated control DNA samples are digested with methylation-sensitive restriction enzymes.
In some embodiments, a sample is separated into at least two portions. The first portion is digested with an enzyme from one of the three possible methylation-sensing classes (i.e., methylation sensitive, methylation insensitive, and methylation dependent). Each additional portion is digested with the isoschizomeric partner from a different methylation-sensing class from the enzyme used to digest the first portion. The intact loci are then amplified and quantified. The relative methylation at the locus can be determined by comparing the results obtained from any two of the reactions to each other, with or without comparison to an undigested portion. In the case where methylation insensitive enzymes are used, the portion must undergo a partial digestion.
In some embodiments, the DNA sample is treated with an agent that modifies unmethylated cytosine, but leaves methylated cytosine unmodified, e.g., sodium bisulfite. The sample is separated into equal portions, and one portion is treated with a methylation-dependent restriction enzyme (e.g., McrBC). Sodium bisulfite treatment does not modify McrBC recognition sites because sodium bisulfite modifies unmethylated cytosine and the recognition site of each McrBC hemi-site is a purine base followed by a methylated cytosine. Samples from both cut and uncut portions are then amplified using at least one primer that distinguishes between methylated and unmethylated nucleotides. The amplified portions are then compared to determine relative methylation. Certain quantitative amplification technologies employ one or more detection probes that are distinct from the amplification primers. These detection probes can also be designed to discriminate between converted methylated and unmethylated DNA. In some embodiments, the detection probes are used in combination with a methylation-dependent restriction enzyme (e.g., McrBC). For example, the detection probes can be used to quantify methylation density within a locus by comparing the kinetic amplification profiles between a converted McrBC treated sample and a converted sample that was not treated with McrBC.
Alternatively, in some embodiments, the sample is divided into equal portions and one portion is digested (partially or completely) with a methylation-dependent restriction enzyme (e.g., McrBC). Both portions are then treated with sodium bisulfite and analyzed by quantitative amplification using a primer that distinguishes between converted methylated and unmethylated nucleotides. The amplification products are compared to each other as well as a standard to determine the relative methylation density.
In some embodiments, the DNA sample is divided into portions and one portion is treated with one or more methylation-sensitive restriction enzymes. The digested portion is then further subdivided and one subdivision is digested with a methylation-dependent restriction enzyme (e.g., McrBC). The various portions and subportions are then amplified and compared. Following digestion, the portions and subportions can optionally be treated with sodium bisulfite and amplified using at least one primer that distinguishes between methylated and unmethylated nucleotides.
In some embodiments, the DNA sample is divided into four portions: a first portion is left untreated, a second portion is contacted with a methylation-sensitive restriction enzyme (wherein intact sequences are methylated), a third portion is contacted with a methylation-dependent restriction enzyme (wherein intact sequences are unmethylated), and a fourth portion is contacted with a methylation-sensitive restriction enzyme and a methylation-dependent restriction enzyme in which one of the restriction enzymes in the fourth portion is contacted to the sample under conditions that allow for at least some copies of potential restriction enzyme cleavage sites in the locus to remain uncleaved (e.g., under partial digest conditions and/or using McrBC). If desired, a fifth portion of the sample can be analyzed following treatment with a methylation insensitive isoschizomer of a methylation-dependent or methylation-sensitive restriction enzyme used in another portion, thereby controlling for incomplete digestions and/or mutations at the restriction enzyme recognition sequence. In addition to digestion, the portions and subportions can optionally be treated with sodium bisulfite and amplified using at least one primer that distinguishes between converted methylated and unmethylated nucleotides.
VIII. Kits
The present invention also provides kits for performing the methods of the invention. For example, the kits of the invention can comprise, e.g., a methylation-dependent restriction enzyme or a methylation sensitive restriction enzyme, a control DNA molecule comprising a pre-determined number of methylated nucleotides, and one or two different control oligonucleotide primers that hybridize to the control DNA molecule. In some cases, the kits comprise a plurality of DNA molecules comprising different pre-determined numbers of methylated nucleotides to enable the user to compare amplification of a sample to several DNAs comprising a known number of methylated nucleotides.
The kits of the invention will often contain written instructions for using the kits. The kits can also comprise reagents sufficient to support the activity of the restriction enzyme. The kits can also include a thermostable DNA polymerase.
In some cases, the kits comprise one or two different target oligonucleotide primers that hybridize to a pre-determined region of human genomic DNA. For example, as described above, the primers can allow for amplification of loci associated with the development or prognosis of disease.
In some embodiments, the kits may comprise one or more detectably-labeled oligonucleotide probes to monitor amplification of target polynucleotides.
In some embodiments, the kits comprise at least one target oligonucleotide primer that distinguishes between modified unmethylated and methylated DNA in human genomic DNA. In these embodiments, the kits also typically include a fluorescent moiety that allows the kinetic profile of any amplification reaction to be acquired in real time.
In some embodiments, the kits comprise at least one target oligonucleotide primer that distinguishes between modified unmethylated and methylated DNA in human genomic DNA. In these embodiments, the kits will also typically include an agent that modifies unmethylated cytosine.
In some embodiments, the kits comprise an RNA probe, a binding agent (e.g., an antibody or an antibody mimetic) that specifically binds RNA:DNA complexes, detection reagents, and methylation sensitive and/or methylation dependent restriction enzymes.
EXAMPLES
Example 1
Comparison to Identify Methylation at a Locus
The following example illustrates how the methods of the invention can be used to determine the number of methylated copies of a locus, the number of unmethylated copies of a locus, the number of hemimethylated copies of a locus, the number of mutated copies of a locus, and the total number of copies of a locus in a population of nucleic acids. The nucleic acids are isolated from a sample and divided into portions, each of which contain all of the sequences present in the sample. This example uses the restriction site for Sau3A I for illustrative purposes and monitors 6 mA methylation. One of skill in the art will appreciate that different enzymes could be selected to monitor cytosine methylation.
Any given restriction site has three potential states: (1) hemimethylated; (2) methylated; (3) unmethylated; and (4) mutated.












1.
G*ATC =
hemimethylated (“hemi”)





CTAG



 



2.
G*ATC =
methylated (“meth”)




CTA*G



 



3.
GATC =
unmethylated (“unmeth”)




CTAG



 



4.
GTTC =
mutated (“mut”)




CAAG






Sau3A I is a methylation insensitive restriction enzyme which cuts when a methylated adenosine residue is at its recognition site. Dpn I is a methylation-dependent restriction enzyme which cuts only when a methylated adenosine residue is at or near its recognition site on both strands. Mbo I is a methylation-sensitive enzyme that does not cut when a methylated adenosine residue is at its recognition site, and is also the isoschizomer of Sau3A I. Hemimethylated sites are cut by Sau3A I, but not by Dpn I or Mbo I; methylated sites are cut by Dpn I and Sau3A I, but not by Mbo I; and unmethylated sites are cut by Sau3A I and Mbo I, but not by Dpn I.
A. Quantitative PCR of a first portion of untreated nucleic acids, or mock treated nucleic acids, from the sample yields the total number of copies of the locus in the sample, which equals:

(1) hemi+(2) meth+(3) unmeth+(4) mut.

B: Cutting a second portion of nucleic acids with the methylation-sensitive restriction enzyme Mbo I, followed by quantitative PCR, leads to amplification of the methylated copies of the locus in the sample, which equals:

(1) hemi+(2) meth+(4) mut.

C: Cutting a third portion of nucleic acids cut with the methylation-dependent restriction enzyme Dpn I followed by quantitative PCR, leads to amplification of the unmethylated copies in the sample, which equals:

(1) hemi+(3) unmeth+(4) mut.

D. Cutting a fourth portion of nucleic acids with the methylation-sensitive restriction enzyme Mbo I, and the methylation-dependent restriction enzyme Dpn I, followed by quantitative PCR leads to leads to amplification of hemimethylated copies in the sample, which equals:

(1) hemi+(4) mut.

E: Cutting a fifth portion of nucleic acids cut with Sau3A I, a methylation-insensitive restriction enzyme that is an isoschizomer of the methylation-dependent restriction enzyme (Dpn I), followed by quantitative PCR, leads to amplification of mutant copies in the sample, i.e., copies which are complementary to the PCR primers, but do not contain hemimethylated, methylated, or unmethylated restriction sites, which equals:

(4) mut.

F. A comparison of the results from A and B leads to the number of unmethylated loci in the sample:

Unmeth=A[hemi+meth+unmeth+mut]−B[hemi+meth+mut].

G. A comparison of the results from A and C leads to the number of methylated copies in the sample:

Meth=A[hemi+meth+unmeth+mut]−C[hemi+unmeth+mut].

H. A comparison of the results from A, B, and C leads to the number of hemimethylated copies and unmethylated copies in the sample:

Hemi+unmeth=C[hemi+unmeth+mut]−(A[hemi+meth+unmeth+mut]−B[hemi+meth+mut]).

Hemi+unmeth=B[hemi+meth+mut]−(A[hemi+meth+unmeth+mut]−B[hemi+unmeth+mut]).

I. A comparison of the results from A and D leads to the number of methylated and unmethylated copies in the sample:

Meth+unmeth=A[hemi+meth+unmeth+mut]−D[hemi+mut].

J. A comparison of the results from D and E leads to the number of hemimethylated copies in the sample:

Hemi=D[hemi+mut]−E[mut].

K. A comparison of the results from E and D with B or C leads to the number of methylated or unmethylated copies in the sample, respectively:

Meth=B[hemi+meth+mut]−E[mut]−(D[hemi+mut]−E[mut])

Unmeth=C[hemi+unmeth+mut]−E[mut]−((D[hemi+mut]−E[mut]).

Example 2
Demonstrating the Sensitivity of Detection
Human male placental DNA was obtained and was methylated in vitro using M.SssI, which methylates cytosines (5mC) when the cytosines are followed by guanosine (i.e., GC motifs). The resulting in vitro methylated DNA was then mixed into unmethylated male placental DNA at known ratios, thereby producing a set of mixes, each comprising a different percentage of total copies that are methylated.
The various mixtures were then divided into three portions: an uncut portion; a portion digested with HhaI, a methylation-sensitive restriction enzyme that is sensitive to 5mC and having the recognition sequence GCGC, where underlined nucleotides are unmethylated; and a portion digested with both HhaI and McrBC. McrBC is a methylation-dependent restriction enzyme that cleaves in the proximity of its methylated recognition sequence. The digested sequences were subsequently amplified using primers specific for a region upstream of the CDKN2A (p16) gene in the human genome-[Ensembl gene ID# ENSG00000147889]. This region was determined to be unmethylated in human male placental DNA that has not been methylated in vitro. The primer sequences were:










Forward primer




5′-CGGGGACGCGAGCAGCACCAGAAT-3′



(SEQ ID NO: 2),



 



Reverse primer



5′ CGCCCCCACCCCCACCACCAT-3′



(SEQ ID NO: 3)






and standard PCR conditions were used:

1 cycle [at 95° C. for 3 minutes]
followed by 49 cycles at [95° C. for 30 sec, 65° C. for 15 seconds, and 68° C. for 15 seconds, a plate read (68° C.) and then another plate read at 83° C.]. The second plate reading at 83° C. was conducted to eliminate the fluorescence contribution of primer dimers to the reaction profile. A melt-curve, which measures fluorescence as a function of temperature, was performed between 80° C. and 95° C. at the end of the cycles and product specificity was determined. The locus of interest is 181 bp in length and has a melting temperature of approximately 89° C. Amplification product accumulation was determined using the intercalating dye, SYBR GreenTM Dynamo Kit from MJ Research, which fluoresces when it binds to double stranded nucleic acids, and reactions were cycled and fluorescent intensity was monitored using the MJ Opticon II Real-time PCR machine.
A threshold at which the signal from the amplification products could be detected above background was determined empirically from a parallel analysis of a template dilution standard curve. The threshold was adjusted to maximize the fit of the regression curve (Ct vs log [DNA]), according to standard cycle threshold determination protocols familiar to those skilled in the art, such as those described in e.g., Fortin et al., Anal. Biochem. 289: 281-288 (2001). Once set, the threshold was fixed and the Ct was calculated by the software (MJ Research Opticon II Monitor V2.02). As expected, the derived cycle thresholds increased at higher dilutions of methylated to unmethylated DNA (FIG. 2). Also shown in FIG. 2, the change (or “shift”) in cycle threshold (ΔCt) between uncut DNA and the HhaI treated DNA corresponded with that expected (E) for the dilutions, demonstrating that cycle threshold shift can be used to accurately predict the relative proportion of copies that are methylated in the sample out of the total number of copies in the sample.
FIG. 2 also illustrates that the addition of HhaI (a methylation sensitive restriction enzyme) and McrBC (a methylation-dependent restriction enzyme) further alters the Ct compared to the samples treated with HhaI alone. The degradation in the number of intact copies, and the resultant Ct shift to a higher Ct value after treatment with the methylation dependent restriction enzyme and the methylation sensitive enzyme further confirms the assessment that the intact copies present after treatment with the methylation-sensitive restriction enzyme alone are in fact methylated. In other words, this double digest provides a control against the possibility that HhaI was not added, was inactive, was partially active, or otherwise did not result in a complete digest. The addition of the methylation-dependent restriction enzyme and its ability to destroy methylated templates confirms the results observed after treatment with just the methylation-sensitive restriction enzyme and provides an internal control to assess the completeness of the methylation-sensitive restriction enzyme reaction.
FIG. 3 depicts the kinetic profile of four portions at three dilution of methylated DNA to unmethylated DNA. In each of the three dilutions, all four portions were digested first with the methylation sensitive restriction enzyme HhaI. The first two portions in each dilution were digested with McrBC, and the second two portions in each dilution were untreated with regards to McrBC. All portions were the amplified under identical conditions and the fluorescence intensities were measured. Three observations can be made. First, the duplicate reactions have nearly identical Ct values, demonstrating that the assays are highly reproducible. Second, decreasing change in cycle threshold between treated and untreated portions as a function of increasing dilution of the methylated copies shows that as the methylated gene copies get more rare, there is less difference between the Ct values observed between McrBC treated and untreated portion. This suggests that the Hha and Hha+McrBC reactions will converge and that at some point we will not be able to monitor methylation density or be able to identify the presence or absence of methylated copies. A theoretical extinction of detection will occur at a ΔCt of zero. Using a regression analysis we solved for the extinction function in our system and found that the dilution where ΔCt=0 is 1:20,000, methylated copies to unmethylated copies respectively. This regression analysis is detailed in FIG. 5.
FIG. 3 shows the fluorescent kinetic profile of a series of portions all diluted to 1:2,000 methylated copies to unmethylated copies, respectively. While the overall fluorescence obtained from the 1:2,000 reactions is not ideal, one can see a difference between the HhaI and the HhaI/McrBC reactions. Notice that the McrBC digestion destroys the accumulation of the fluorescence, and the melting point curve in FIG. 4 shows a specific peak at 89° C., which is the predicted melting temperature for the 181 bp specific amplicon. Here we are clearly detecting merely 1.4 cellular equivalents of methylated DNA diluted into a total of 2,762 cellular equivalents of DNA.
As shown in FIG. 5, 1.4 cellular equivalents (CE) were detected out of a total of 2764 CE in the tube having a total of 20 ng of genomic DNA. Each cellular equivalent has approximately 7.9 pg of genomic DNA/per cell. Thus, if 50 ng of genomic DNA is used, one methylated copy in the presence of 10,000 unmethylated copies should be detectable. This principle is illustrated in FIG. 5. FIG. 6 provides a breakdown of this analysis. Note that this detection limit may be further lowered by (i) using an optimized FRET-based probe, rather than an intercalating dye, to detect amplified products, (ii) by further optimizing PCR primer design, or (iii) by further optimizing PCR reaction conditions.
Example 3
Constructing a DNA Methylation Standard Sample Set
A standard sample set is generated in numerous ways. For example, a methylase (e.g., M.SssI or other methylases such as M.HhaI, M.AluI) is applied in vitro to a series of DNA samples to produce a standard set of DNAs known to have increasing methylation densities. This standard set is generated by first obtaining a sample of known sequence (e.g., the locus of interest). Next, the sample is divided into a series of samples and each sample in the series is treated with the chosen methylase in the presence of magnesium and in a manner that results in increasing methylation densities of the samples in the series.
A partial methylation reaction refers to contacting DNA with a cocktail of one or more methylases under appropriate reaction conditions such that the methylase modifies some (e.g., about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%) but not all of the possible methylase recognition sites for each enzyme in the methylase cocktail. A DNA sequence is partially methylated by treating DNA with an active methylase for a shorter period of time than is necessary to achieve complete methylation, and then terminating the reaction, or under other altered reaction conditions that allow for the desired amount of partial methylation.
The methylation densities of each sample in the series are measured by sequencing a statistically significant sample of clones from a bisulfite-treated portion of each series member in the set, by identifying the converted cytosines within each clone, and by calculating the average methylation density for each reaction within the methylation sample set. In order to achieve a partial methylation density on a given fragment, the methylase acts in a stochastic manner, and not a processive manner. For M.SssI, this is achieved by conducting the reaction in the presence of magnesium, since M.SssI methylates DNA in a processive way in the absence of magnesium, while in the presence of magnesium, the enzyme methylates CpGs in a nonprocessive, stochastic manner.
Example 4
Quantitatively Determining the Relative Methylation of a Locus of Interest between One Tissue and Another Tissue with Quantitative Amplification
DNA is collected from two sources: a test population (diseased) and a control population (normal).
Each population of DNA fragments is similarly submitted to various partial or complete digestions with the enzyme McrBC. McrBC recognizes two RMC sites, each a half site, that are within 20 to 4,000 bases with an optimal separation of the half sites of 50-103 bp and then cuts the DNA fragment sometimes 3′ of both half sites, sometimes 3′ of the 5′ most half site and 5′ of the 3′ most half sites, and sometimes 5′ of both half sites.
Next, the digested DNA in each population is amplified and the amount of the amplified locus is measured as a function of cycle number. The greater the number of methylated half sites in the locus of interest on a given DNA fragment within the population studied, the greater the probability that McrBC will cut between the PCR primers, and, therefore, a greater number of amplification cycles will be required to achieve the identical concentration of amplified PCR locus.
To determine whether the locus of interest within the test population is more or less methylated than the locus of interest within the control population, a concentration curve of amplified DNA of the test population is compared to the concentration curve of amplified DNA from the control population. Concentration curves reflect the amount of intact DNA as a function of the amount of digestion in a series of different partial digestions.
Example 5
Measuring the Methylation Density at a Locus of Interest within a Tissue with Quantitative Amplification
DNA is obtained from a single source, and is divided into two populations. The first population of DNA is completely digested with the enzyme McrBC, while the remaining population is untreated. Alternatively, the first population is digested with a cocktail of one or more methylation sensitive restriction enzymes (e.g., HpaII, HhaI, or AciI, etc.), while the second population of DNA is untreated.
Next, the digested DNA in the first population is amplified and the amount of the amplified locus is measured as a function of cycle number. The greater the number of methylated half sites in the locus of interest on a given DNA fragment within the population studied, the greater the probability that McrBC will cut between the PCR primers, and, therefore, a greater number of amplification cycles will be required to achieve the identical concentration of amplified PCR locus. Alternatively, when a cocktail of methylation sensitive restriction enzymes is used, the greater the number of methylated restriction sites in the locus of interest on a given DNA fragment within the population studied, the lower the probability that the methylation sensitive cocktail of enzymes will cut between the PCR primers. Therefore, a lower number of amplification cycles will be required to achieve the identical concentration of amplified PCR locus.
To determine whether the locus of interest within the first population is methylated, a comparison is made between the kinetics of the amplification reaction profiles from the treated and untreated populations. Alternatively, to determine the density of methylation within the tissue at the locus of interest, the kinetics of the amplification reaction profiles are compared to those obtained from a known in vitro generated methylation sample set, i.e., a standard methylation curve.
Example 6
Measuring the Methylation Density at a Locus of Interest within a Tissue with Amplification End Point Analysis
DNA is obtained from a single source, and is divided into a series of two or more portions.
This series is exposed to an increasing amount of partial digestion by a methylation dependent restriction enzyme, such as McrBC. The first portion of DNA fragments is untreated, the second portion is lightly digested with McrBC, and subsequent populations are more fully digested (but less than completely) with McrBC. The range of partial digestions is obtained through the manipulation of reaction conditions, such as the titration of enzyme amounts, digestion times, temperatures, reactants, buffers, or other required components.
Next, the DNA from the series of portions are amplified and the amount of amplified PCR loci is measured after a fixed number of cycles. The greater the number of methylated half sites in the locus of interest on a given DNA fragment within the first McrBC-treated portion, the greater the probability that McrBC will cut fragments of the first part between the PCR primers, and the greater number of amplification cycles will be required to detect a certain concentration of amplified PCR locus in the first portion.
To determine whether the locus of interest within the test population is more or less methylated, the results obtained from the series of portions and the parallel analysis of the standard sample set are compared (see Example 3).
Example 7
Quantifying Methylation Using Methylation-Sensing Isoschizomeric Partners and Quantitative PCR
DNA is collected from two sources: a test population (diseased) and a control population (normal). Each population is divided into groups of two or more portions. Each group is exposed to an increasing amount of partial digestion by a methylation sensitive restriction enzyme (e.g., HpaII, MboI (A)). The first portion of DNA fragments is untreated, the second portion is lightly digested with the methylation sensitive restriction enzyme, and subsequent populations are more fully digested (but less than to completion) with the enzyme. The range of partial digestions is obtained through the manipulation of reaction conditions, such as the titration of enzyme amounts, digestion times, temperatures, reactants, buffers, or other required components.
The second group of portions is similarly digested with an isoschizomeric partner of a different methylation-sensing class from the enzyme used to treat the first group of portions (e.g., MspI and Sau3AI (A), respectively). Alternatively, the second group of portions remains untreated.
Next, all of the portions in the groups are amplified and the kinetic reaction profile from each amplification is obtained. Alternatively, end point analysis after a fixed number of cycles is used.
To determine whether the locus of interest within the test population is more or less methylated, a comparison is made between the kinetic reaction profiles between the groups (group vs. group). Additionally, to determine whether the locus of interest between the two tissues is more or less methylated, a comparison is made between the kinetic reaction profiles between the populations (diseased groups vs. normal groups).
Example 8
Quantifying the Methylation Density of a Locus of Interest Using a Cocktail of Methylation Sensitive Enzymes
DNA is obtained from a single source and is divided into groups of two or more portions. Alternatively, DNA is collected from two sources: a test population (diseased) and a control population (normal), and is divided into groups of two or more uniform portions.
The groups of uniform portions are treated with a fixed number of units of a cocktail of one of more methylation sensitive restriction enzymes (e.g., HpaII, HhaI, or AciI) for varied amounts of time.
Next, all of the portions in the groups are amplified and the kinetic reaction profile from each amplification is obtained. Alternatively, end point analysis after a fixed number of cycles is used.
To determine whether the locus of interest within the test population is more or less methylated, a comparison is made between the kinetic reaction profiles between the groups (group vs. group). Additionally, to determine whether the locus of interest between the two tissues is more or less methylated, a comparison is made between the kinetic reaction profiles between the populations (diseased groups vs. normal groups). Finally, the overall amount of methylation can be determined by comparing these results to those obtained from the standard sample set (see Example 3).
Example 9
Quantifying the Methylation Density of a Small Population of Methylated Alleles in the Presence of a Large Population of Unmethylated Alleles
DNA is obtained from a single source and is divided into two portions. Alternatively, DNA is collected from two sources: a test population (diseased) and a control population (normal), and each population is divided into two portions.
To discriminate between methylated and unmethylated alleles, one portion from each population is treated with sodium bisulfite, which converts the unmethylated cytosine residues to uracil, leaving unconverted methylated cytosine residues. The bisulfite-treated portion is divided into two equal subportions. Alternatively, one portion from each population is digested with a cocktail of one or more methylation sensitive restriction enzymes (e.g., HpaII, HhaI, etc.), leaving the remaining portion untreated. The digested portion is similarly divided into two equal subportions.
One of the bisulfite-treated subportions is completely digested with the enzyme McrBC, while the remaining subportion is untreated. Alternatively, one of the methylation sensitive restriction enzyme-treated subportions is completely digested with the enzyme McrBC, while the remaining subportion is untreated.
One or both of the amplification primers are designed to resemble the bisulfite converted sequence overlapping at least one methylated cytosine residue. In this way, only those fragments that belong to the subset of fragments that were methylated at that primer in the test population have the potential of becoming amplified, while those fragments in the subset of fragments that remained unmethylated in the locus of interest will not be amplified. Alternatively, if methylation sensitive enzymes are used to discriminate between methylated and unmethylated alleles, then primers designed to the native sequence are used and only alleles that were methylated at the recognition sites remain intact and will be amplified.
Next, the DNA from both the McrBC-treated and McrBC-untreated portions, along with the relevant controls, are amplified and the amount of amplified PCR loci are measured as a function of cycle number.
To determine whether the locus of interest within the first population is methylated, a comparison is made between the kinetics of the amplification reaction profiles from the treated and untreated populations. To determine the density of methylation within the tissue at the locus of interest, the kinetics of the amplification reaction profiles are compared to those obtained from a known in vitro generated methylation sample set, i.e., a standard methylation curve.
Alternatively, this Example could also be performed by reversing the order of the sodium bisulfite conversion and the McrBC-digestion steps described above (i.e., McrBC digestion takes place prior to sodium bisulfite conversion).
In another alternative, partial digestion using McrBC is used in either a subportion or a series of subportions, instead of complete digestion.
Example 10
Detecting Methylation Density
This example demonstrates determining the average density of methylation (i.e., the average number of methylated nucleotides) within a locus. As provided in FIG. 7, it is likely that in many diseases, methylation of one or more loci goes through a progression of increased methylation density corresponding to disease progression. Previously-described methylation detection techniques involve detecting the presence or absence of methylation at one or more particular nucleotides but do not provide analysis of density across a locus. In contrast, the present invention provides methods for detecting the average number of methylation events within a locus.
As illustrated in FIGS. 12-13, methods that detect methylation at only specific short sequences (typically relying on primer or probe hybridization) may miss changes in methylation (see FIG. 12) that the present methylation density detection methods (which examine relative methylation across an entire locus) are able to detect (see FIG. 13).
This discovery works by treating a locus with a methylation-dependent or methylation-sensitive restriction enzyme under condition such that at least some copies of potential restriction enzyme cleavage sites in the locus to remain uncleaved. While these conditions can be achieved by allowing for partial digestion of a sample, the particular recognition and cutting activity of McrBC allows for additional options.
As discussed above, when two McrBC complexes meet, restriction occurs, typically within  ̃32 bp of either half site (i.e., in one of four regions). See, FIG. 8. Restriction does not occur if half sites are closer than 20 bp.
Since McrBC randomly cuts 5′ or 3′ of the recognized pair of half sites, the probability of cutting at a locus (spanned by primers in the case PCR) is function of the number of methylated half-sites present at or near the locus. For a set concentration of enzyme and time of incubation, the more methylation sites within a locus, the greater the probability McrBC will cut at the locus (or between the primers in the case of PCR). However, under ideal circumstances and sufficient number of DNA copies, the probability that McrBC will cut every copy of a locus is low because it will sometimes cut at a distance outside of the locus, thereby leaving the locus intact. Thus, the number of intact loci is inversely proportional to the average number of methylated nucleotides within the locus. The number of intact loci is inversely proportional to the Ct value for sample. Thus, the Ct value is proportional to the average number of methylated nucleotides within a locus. Thus, comparison of the Ct value of amplified McrBC-treated DNA compared to the Ct value from amplified untreated DNA allows for the determination of methylation density of the locus.
Two aliquots of BAC DNA containing the p16 locus was in vitro methylated at different densities. The first aliquot was densely methylated with M.sssI. There are 20 M.sssI methylase sites within the PCR amplicon, 11 of which are also McrBC half-sites. The second aliquot was sparsely methylated with M.HhaI. There are four M.HhaI methylase sites within the PCR amplicon, all four of which are also McrBC half-sites. Within the PCR amplicon there are also 4 restriction sites for HhaI. All four of these HhaI restriction sites are methylase sites for both M.sssI and M.HhaI, such that complete treatment with either methylase will protect all four HhaI sites from restriction. A different number of units of McrBC was used for a set period of time (four hours) to generate a series of progressively more partial digestions to identify an amount of enzyme to best allow for distinguishing results from the sparsely and densely-methylated DNA. As displayed in FIGS. 9 and 10, the Ct values were proportional to the concentration of McrBC used in both sparsely and densely-methylated sequences. FIG. 11 demonstrates results from titrating different amounts of McrBC to enhance resolution between sparsely and densely methylated sequences to distinguish between the two. In FIG. 11, “1×” equals 0.8 units of McrBC.
The densely methylated target has 2.75-fold more methylated McrBC half sites than the sparsely methylated target (11/4=2.75). Therefore, upon treatment with McrBC and subsequent amplification, we expect to see a different between the Ct of the reactions of about 1.46, because 2ΔCt=2.75. We observed ΔCt (sparse-dense @ 1×McrBC) was 1.51±0.05. Thus, the methylation density of a locus was determined using this method.
Example 11
Methylation Density Determination
This example demonstrates the ability of methylation-dependent and methylation-sensitive restriction enzymes to distinguish different methylation densities at a locus.
A 703 bp portion of the promoter of p16 was amplified. The portion was methylated in vitro in a time course with M.SssI under conditions that promote stochastic methylation. The portion is illustrated in FIG. 14. From the large methylation reaction at different time points, fixed volumes (20 μl) were removed and the methylation reactions were stopped with heat (65° C.). We stopped one reaction before it began (T=1 is 0 minutes methylation, i.e., the unmethylated control; T=2 was stopped at 2 minutes; T=3 was stopped at 5 minutes; and T=4 was stopped at 60 minutes, a time at which the PCR product in the reaction should have been fully methylated.
The reactions were purified and each amplicon then was diluted more than 1 million fold in TE buffer, and was added back to the human genome at a ratio that should approximate a normal copy balance (i.e., two copies per 7.9 picograms). The human genome used was homozygous for a deletion of the p16 gene. The deletion cell line is CRL-2610. This allowed us to add a fixed amount of the human genome (i.e., control for the complexity of the genome in our reaction).
DNA samples were cleaved with Aci I (a methylation-sensitive restriction enzyme), McrBC (a methylation-dependent restriction enzyme), or both as double digest, and the portion was amplified. Amplicons were detected with the MS_p16(207) SYBR green real-time PCR system. Twenty nanograms of input DNA (genome +amplicon) equal  ̃2764 cellular equivalents/per PCR reaction. Each set of four digests was brought up to volume in restriction salts with BSA and GTP such that it could be split into four tubes ( ̃4 μg). Each of the four digest tubes ( ̃1 μg) had 100 μl total volume such that 2 μl could be added to PCR reactions, thereby adding 20 ng of DNA. Digests were allowed to proceed for four hours and were heat killed for 20 minutes. PCR conditions:










The forward primer was




CAGGGCGTCGCCAGGAGGAGGTCTGTGATT



(SEQ ID NO: 4).



 



The reverse primer was



GGCGCTGCCCAACGCACCGAATAGTTACGG



(SEQ ID NO: 5).






Dynamo MJ qPCR buffer, 65° C. anneal, two cycle PCR (95° C. 30 sec, 65° C. 20 sec) cycled 49 times and monitored with an MJ opticon II quantitative PCR system.
We hypothesized that if the technology is monitoring density:

    a) The McrBC cleavage should demonstrate a larger ΔCt for each sample in a progression from 0 ΔCt for T=1, up to a maximal ΔCt at T=4 (60 minutes)
    b) The Aci I reactions should demonstrate the converse relationship.
    c) The mock treated and double digests should be fixed reference points


As illustrated in FIG. 15, we observed the trends outlined above. The McrBC curve moves oppositely from the Aci I curve, and the movement is proportional with the increasing methylation content in the locus. The untreated and double digests indicate the boundaries of the assay field. The system resolves the difference between each of the reactions along the time course, such that each graphical depiction showing the various timed reactions is different. The point where the profile intersects the dashed threshold line indicates the point where information is compared.
Another way to visualize the data is by plotting the change in cycle threshold values (ΔCt). See, FIG. 16. FIG. 16 displays the ΔCt for McrBC-treated compared to untreated at each time point in the partial methylation reaction, and the corresponding ΔCt for the Aci I digests (Aci I compared to untreated). As expected, the McrBC and Aci I ΔCt lines provide an intersecting inverse pattern. The Aci I graph displays a chunky shape because its cut sites are fixed, while McrBC displays a smooth continuous distribution, reflecting its ability to cut more or less randomly following site recognition. Frequency of cutting is proportional to the expected change in methylation occupancy based upon the time course. The error bars associated with the real-time measurements are indicated. If they are not visualized, they are within the data point.
Example 12
Monitoring DNA Methylation of a Target Sequence Present at Multiple Locations in the Genome
This example demonstrates the ability of the present technology to determine the methylation of a target sequence that is present in a genome more than one time (i.e., more than one copy) using an assay that monitors a sequence repeated in the kafirin gene cluster in Sorgum bicolor. 
Eleven kafirin genes were annotated from the publicly available sequence of a BAC clone AF527808 from Sorghum bicolor. PCR primers were designed to amplify a 247 bp amplicon from all 11 kafirin genes (the primer sequences were conserved in all 11).










The forward primer was




5′ CTCCTTGCGCTCCTTGCTCTTTC 3′



(SEQ ID NO: 6).



 



The reverse primer was



5′ GCTGCGCTGCGATGGTCTGT 3′



(SEQ ID NO: 7).






Sorghum genomic DNA isolated from seedling leaf was divided into 6 equal portions. The six portions were treated in the following manner: i) untreated (mock treated), ii) HhaI digested, iii) McrBC digested, iv) HhaI and McrBC digested, v) PstI digested and, vi) PstI and McrBC digested. Equal volume aliquots from the six portions were amplified using the above PCR primers in the following manner:
The SYBR green real-time PCR cycling parameters were 95° C. for 3 minutes, followed by 50 cycles of 2 step PCR 95° C. for 30 sec, 56° C. for 30 seconds with the Dynamo Kit from MJ Research (Boston, Mass.). We utilized both a low temperature (70° C.) and a high-temperature plate read (82° C.). The input of genomic DNA was 10 ng per PCR reaction. The threshold was set using a template dilution standard control.
The kinetic profiles for the 6 PCR reactions are depicted in FIG. 18. The inset in FIG. 18 depicts the template dilution standard curve used to set the cycle threshold for the experiment. Each set of 6 digests was performed three times, and each of the 18 digests had four PCR replicates. The PCR reactions were determined to be highly reproducible. In FIG. 18, PCR amplification reaction kinetics for each of the six digestions are depicted with different colors: Red =mock treated, Blue=McrBC digested, Orange=HhaI digested, and Green=HhaI+McrBC double digest, Pink=PstI, and Azure=PstI+McrBC double-digest. Comparisons between the cycle thresholds of the six amplified digestions were made and of the density of CNG and CG methylation in the repeated target sequence was determined.
In all 11 kafirin genes, all PstI sites in the repeated target sequence were methylated (at CNG) and PstI digestion was blocked since the PstI treated sample (pink) has the same cycle threshold (Ct) as the mock treated sample (red). This result is supported by the McrBC digested sample (blue), which has a significantly higher Ct than the mock-digested DNA control (red), further demonstrating that CNG methylation exists because McrBC was able to cut, thereby lowering the number of intact copies of the target sequence. All, or almost all, of the PstI sites are methylated because the double PstI+McrBC digest (light blue) has the same Ct as McrBC alone (blue). Note that the McrBC digestion with and without PstI yields the same Ct, while HhaI with McrBC (green) yields a higher Ct on average; suggesting that not all HhaI sites were methylated and that HhaI was able to reduce the number of intact copies of the target sequence. These results indicate that every target sequence has high CNG methylation covering all PstI sites, while some but not all HhaI sites are methylated, indicating partial CG methylation of HhaI sites in the target sequence. The specificity of each reaction was confirmed using melt-curve analysis.
For the kafirin genes, the average difference in Ct between the McrBC single and HhaI+McrBC double digests is 2.46 cycles (22.08±0.34 HhaI+McrBC−19.62±0.19 McrBC). We compared the cycle-thresholds of genomic DNA that had been subjected to various treatments and inferred methylation occupancy through the changes in Ct mediated by the treatments. The Ct of any locus is a function of the number of copies present within the assay tube. Each of the eleven genes was broken into  ̃1.5 kb pieces which were aligned to create a consensus kafirin assembly (FIG. 17). The consensus kafirin sequence was examined and PCR primers amplifying a 247 bp amplicon were selected (see above).
As for CG methylation, the HhaI digested (orange) sample has the same Ct as the mock treated control (red); however, the HhaI+McrBC double digest (green) has a Ct that is 2.46 cycles greater than the McrBC alone (blue), indicating that some HhaI sites must not be modified. A cycle threshold difference of 2.46 indicates that there is 22.46, or approximately 5.5-fold, less DNA in the HhaI+McrBC double digested sample. This suggests that 2 out of the 11 kafirin genes have some unmethylated HhaI sites.
To independently confirm the presence of methylation at the repeated target sequence, a 1× shotgun sequence was generated of the methyl filtered sorghum genome (See U.S. patent Publication No. 20010046669), Bedell et al., PLOS in press). 95% of the genes in the sorghum genome were determined to be represented in the methyl filtered sequence set. In the kafirin gene cluster, however, only 2 of 11 genes from BAC clone AF527808 were represented in the methyl filtered sequence set, suggesting that most or all of them may be methylated, and therefore are underrepresented in the methyl filtered sequence. Ten of the genes are tandemly arrayed in a cluster and share an average of 99.1% sequence identity, while the eleventh gene is located 45 kb away and is more diverged (76.2% identity on average). A 247 bp region was selected for PCR close to the 5′ end because of its near identity across all 11 genes and because of the high CG and CNG content (see FIG. 17). The independent confirmation of methylation at the target sequence agreed with the methylation determination made by analysis of the reaction kinetics of the amplified digested DNA.
The above examples are provided to illustrate the invention but not to limit its scope. Other variants of the invention will be readily apparent to one of ordinary skill in the art and are encompassed by the appended claims. All publications, databases, and patents cited herein are hereby incorporated by reference in their entirety for all purposes.

## Claims

1. A method of detecting the quantity of methylation at a locus within a population of nucleic acids, the method comprising
(a) dividing the population of nucleic acids into at least two physically distinct portions, thereby generating at least a first portion and a second portion,
(b) after step (a), contacting the first portion with a methylation-sensitive restriction enzyme to obtain a population comprising fragmented unmethylated copies of the locus and intact methylated copies of the locus;
(c) quantifying the intact copies of the locus in the first portion in the presence of the fragmented unmethylated copies of the locus, wherein the quantifying step comprises quantitative amplification;
(d) after step (a), contacting the second portion with a methylation-dependent restriction enzyme to obtain a population comprising fragmented methylated copies of the locus and intact unmethylated copies of the locus, wherein the methylation-dependent restriction enzyme is contacted to the second portion under conditions that allow for at least some copies of potential restriction enzyme cleavage sites for the methylation-dependent restriction enzyme in the locus to remain uncleaved;
(e) quantifying the intact copies of the locus in the second portion in the presence of the fragmented unmethylated copies of the locus, wherein the quantifying step comprises quantitative amplification; and
(f) determining the quantity of methylation at the locus by comparing the number of intact copies of the locus in the first portion and number of intact copies of the locus in the second portion.

2. The method of claim 1, further comprising
quantifying a third portion of the nucleic acids, thereby amplifying the total intact copies of the locus in the population; and
comparing the number of total intact copies of the locus to the number of intact copies of the locus in the first portion and/or intact copies of the locus in the second portion.

3. The method of claim 1, further comprising contacting a third portion of the nucleic acids with a methylation-dependent restriction enzyme and a methylation-sensitive restriction enzyme;
quantifying copies of the intact locus in the third portion; and
determining the presence of methylation at the locus by comparing the number of the intact copies of the locus in the third portion to the number of intact copies of the locus in the first portion and/or intact unmethylated copies of the locus in the second portion.

4. The method of claim 2, further comprising contacting a fourth portion of the nucleic acids with a methylation-dependent restriction enzyme and a methylation-sensitive restriction enzyme;
quantifying intact copies of the locus in the fourth portion; and
determining the presence of methylation at the locus by comparing the number of intact copies of the locus in the fourth portion to the number of total intact copies of the locus in the third portion and/or intact copies of the locus in the first portion and/or intact copies of the locus in the second portion.

5. The method of claim 1, further comprising identification of mutations within the locus.

6. The method of claim 5, wherein a fifth portion of the nucleic acids is contacted with a methylation-insensitive restriction enzyme;
quantifying intact copies of the locus in the fifth portion to obtain a population of nucleic acids comprising a mutation at the locus; and
determining the presence of a mutation at the locus by comparing the number of the intact copies of the locus in the fifth portion to the number of intact copies of the locus in the fourth portion and/or total intact copies of the locus in the third portion and/or intact copies of the locus in the first portion and/or intact copies of the locus in the second portion.

7. The method of claim 2, wherein the determining step (f) comprises subtracting the number of intact copies of the locus remaining after the first portion is cut with the methylation-sensitive restriction enzyme from the total intact copies of the locus.

8. The method of claim 2, wherein the determining step (f) comprises subtracting the number of intact copies of the locus remaining after the second portion is cut with the methylation-dependent restriction enzyme from the total intact copies of the locus.

9. The method of claim 2, wherein the determining step (f) comprises:
(a) subtracting the number of intact copies of the locus remaining after the first portion is cut with the methylation-sensitive restriction enzyme from the total intact copies of the locus, thereby determining the number of unmethylated copies of the locus; and
(b) subtracting the number of unmethylated copies of the locus from the number of intact copies of the locus remaining after the second portion is cut with the methylation-dependent restriction enzyme, thereby determining the number of hemimethylated and mutant copies of the locus.

10. The method of claim 2, wherein the determining step (f) comprises:
(a) subtracting the number of intact copies of the locus remaining after the second portion is cut with the methylation-dependent restriction enzyme from the total intact copies of the locus, thereby determining the number of methylated copies of the locus; and
(b) subtracting the number of methylated copies of the locus from the number of intact copies of the locus remaining after the first portion is cut with the methylation-sensitive restriction enzyme, thereby determining the number of hemimethylated and mutant copies of the locus.

11. The method of claim 4, wherein the determining step (f) comprises subtracting the number of intact copies of the locus remaining after the fourth portion is cut with the methylation-dependent restriction enzyme and the methylation-sensitive restriction enzyme from the total intact copies of the locus, thereby determining the number of methylated and unmethylated copies of the locus.

12. The method of claim 6, wherein a number of hemimethylated copies of the locus is determined by subtracting the number of intact loci remaining after the fifth portion of the nucleic acids is contacted with a methylation-insensitive restriction enzyme from the number of intact copies of the locus remaining after the fourth portion is cut with the methylation-dependent restriction enzyme and the methylation-sensitive restriction enzyme.

13. The method of claim 6, wherein the number of methylated copies of the locus is determined by:
(a) subtracting the number of intact copies of the locus remaining after the fifth portion of the nucleic acids is contacted with a methylation-insensitive restriction enzyme from the number of intact copies of the locus remaining after the fourth portion is cut with the methylation-dependent restriction enzyme and the methylation-sensitive restriction enzyme, thereby determining the number of hemimethylated copies of the locus; and
(b) subtracting the number of hemimethylated copies of the locus and the number of intact copies of the locus remaining after the fifth portion of the nucleic acids is contacted with the methylation-insensitive restriction enzyme from the number of intact copies of the locus remaining after the first portion of nucleic acids is contacted with the methylation-sensitive restriction enzyme, thereby determining the number of methylated copies of the locus.

14. The method of claim 6, wherein the number of unmethylated copies of the locus is determined by:
(a) subtracting the number of intact copies of the locus remaining after the fifth portion of the nucleic acids is contacted with a methylation-insensitive restriction enzyme from the number of intact copies of the locus remaining after the fourth portion is cut with the methylation-dependent restriction enzyme and the methylation-sensitive restriction enzyme, thereby determining the number of hemimethylated copies of the locus; and
(b) subtracting the number of hemimethylated copies of the locus and the number of intact copies of the locus remaining after the fifth portion of the nucleic acids is contacted with the methylation-insensitive restriction enzyme from the number of intact copies of the locus remaining after the second portion of nucleic acids is contacted with the methylation-dependent restriction enzyme, thereby determining the number of unmethylated copies of the locus.

15. The method of claim 2, wherein the quantifying steps comprise quantitative amplification.

16. The method of claim 3, wherein the quantifying steps comprise quantitative amplification.

17. The method of claim 4, wherein the quantifying steps comprise quantitative amplification.

18. The method of claim 6, wherein the quantifying steps comprise quantitative amplification.

19. The method of claim 1, wherein the nucleic acids are contacted with an agent that modifies unmethylated cytosines before the amplification step;
and the intact copies of the locus are amplified with a pair of oligonucleotide primers comprising at least one primer that distinguishes between modified methylated and unmethylated DNA.

20. The method of claim 15, wherein the nucleic acids are contacted with an agent that modifies unmethylated cytosines before the amplification step;
and the intact copies of the locus are amplified with a pair of oligonucleotide primers comprising at least one primer that distinguishes between modified methylated and unmethylated DNA.

21. The method of claim 16, wherein the nucleic acids are contacted with an agent that modifies unmethylated cytosines before the amplification step;
and the intact copies of the locus are amplified with a pair of oligonucleotide primers comprising at least one primer that distinguishes between modified methylated and unmethylated DNA.

22. The method of claim 17, wherein the nucleic acids are contacted with an agent that modifies unmethylated cytosines before the amplification step;
and the intact copies of the locus are amplified with a pair of oligonucleotide primers comprising at least one primer that distinguishes between modified methylated and unmethylated DNA.

23. The method of claim 18, wherein the nucleic acids are contacted with an agent that modifies unmethylated cytosines before the amplification step;
and the intact copies of the locus are amplified with a pair of oligonucleotide primers comprising at least one primer that distinguishes between modified methylated and unmethylated DNA.

24. The method of claim 19, wherein the agent is sodium bisulfite.

25. The method of claim 20, wherein the agent is sodium bisulfite.

26. The method of claim 21, wherein the agent is sodium bisulfite.

27. The method of claim 22, wherein the agent is sodium bisulfite.

28. The method of claim 23, wherein the agent is sodium bisulfite.

29. The method of claim 3, wherein the methylation-dependent restriction enzyme is contacted to the third portion under conditions that allow for at least some copies of potential restriction enzyme cleavage sites for the methylation-dependent restriction enzyme in the locus to remain uncleaved.

30. The method of claim 4, wherein the methylation-dependent restriction enzyme is contacted to the fourth portion under conditions that allow for at least some copies of potential restriction enzyme cleavage sites for the methylation-dependent restriction enzyme in the locus to remain uncleaved.

31. The method of claim 1, wherein the locus has a density of methylation and the density of methylation at the locus is determined by comparing the number of intact methylated loci in the second portion after cleavage with a control value representing the quantity of methylation in a control DNA.

32. The method of claim 29, wherein the locus has a density of methylation and the density of methylation at the locus is determined by comparing the number of intact methylated loci in the third portion after cleavage with a control value representing the quantity of methylation in a control DNA.

33. The method of claim 30, wherein the locus has a density of methylation and the density of methylation at the locus is determined by comparing the number of intact methylated loci in the fourth portion after cleavage with a control value representing the quantity of methylation in a control DNA

34. The method of claim 1, wherein the methylation-sensitive restriction enzyme is contacted to the first portion under conditions that allow for at least some copies of potential restriction enzyme cleavage sites for the methylation-sensitive restriction enzyme in the locus to remain uncleaved.

35. The method of claim 2, wherein the methylation-sensitive restriction enzyme is contacted to the first portion under conditions that allow for at least some copies of potential restriction enzyme cleavage sites for the methylation-sensitive restriction enzyme in the locus to remain uncleaved.

36. The method of claim 3, wherein the methylation-sensitive restriction enzyme is contacted to the third portion under conditions that allow for at least some copies of potential restriction enzyme cleavage sites for the methylation-sensitive restriction enzyme in the locus to remain uncleaved.

37. The method of claim 4, wherein the methylation-sensitive restriction enzyme is contacted to the third portion under conditions that allow for at least some copies of potential restriction enzyme cleavage sites for the methylation-sensitive restriction enzyme in the locus to remain uncleaved.

38. The method of claim 34, wherein the density of methylation at the locus is determined by comparing the number of intact unmethylated loci in the first portion after cleavage with a control value representing the quantity of methylation in a control DNA.

39. The method of claim 35, wherein the density of methylation at the locus is determined by comparing the number of intact unmethylated loci in the first portion after cleavage with a control value representing the quantity of methylation in a control DNA.

40. The method of claim 36, wherein the density of methylation at the locus is determined by comparing the number of intact unmethylated loci in the third portion after cleavage with a control value representing the quantity of methylation in a control DNA.

41. The method of claim 37, wherein the density of methylation at the locus is determined by comparing the number of intact unmethylated loci in the third portion after cleavage with a control value representing the quantity of methylation in a control DNA.

42. The method of claim 3, wherein the methylation-dependent restriction enzyme is contacted with the third portion under conditions that allow for at least some copies of potential restriction enzyme cleavage sites for the methylation-dependent restriction enzyme in the locus to remain uncleaved.

43. The method of claim 42, wherein the density of methylation at the locus is determined by comparing the number of intact methylated loci in the fourth portion after cleavage with a control value representing the quantity of methylation in a control DNA.

44. The method of claim 3, wherein the methylation-sensitive restriction enzyme is contacted with the third portion under conditions that allow for at least some copies of potential restriction enzyme cleavage sites for the methylation-sensitive restriction enzyme in the locus to remain uncleaved.

45. The method of claim 44, wherein the density of methylation at the locus is determined by comparing the number of intact unmethylated loci in the fourth portion after cleavage with a control value representing the quantity of methylation in a control DNA.

46. The method of claim 1, wherein the methylation is at the C5 position of a cytosine within the locus.

47. The method of claim 1, wherein the nucleic acids are DNA.

48. The method of claim 47, wherein the DNA is genomic DNA.

49. The method of claim 1, wherein the methylation-sensitive restriction enzyme does not cut when a cytosine within the recognition sequence is methylated at position C5.

50. The method of claim 49, wherein the methylation-sensitive restriction enzyme is selected from the group consisting of: Aat II, Aci I, Ac1 I, Age I, Alu I, Asc I, Ase I, AsiS I, Bbe I, BsaA I, BsaH I, BsiE I, BsiW I, BsrF I, BssH II, BssK I, BstB I, BstN I, BstU I, Cla I, Eae I, Eag I, Fau I, Fse I, Hha I, HinP1 I, HinC II, Hpa II, Hpy99 I, HpyCH4 IV, Kas I, Mbo I, Mlu I, MapA1 I, Msp I, Nae I, Nar I, Not I, Pml I, Pst I, Pvu I, Rsr II, Sac II, Sap I, Sau3A I, Sfl I, Sfo I, SgrA I, Sma I, SnaB I, Tsc I, Xma I, and Zra I.

51. The method of claim 1, wherein the methylation-dependent restriction enzyme is McrBC.

52. The method of claim 1, wherein the first portion of nucleic acids is further contacted with at least a second methylation-sensitive enzyme.

53. The method of claim 1, wherein the second portion of nucleic acids is further contacted with at least a second methylation-dependent enzyme.

54. The method of claim 1, wherein the methylation-sensitive restriction enzyme is methyl-cytosine sensitive.

55. The method of claim 1, further comprising contacting a third portion of the nucleic acids with a second methylation-sensitive restriction enzyme and contacting a fourth portion of the nucleic acids with a second methylation-dependent restriction enzyme;
quantifying intact loci in the third and fourth portions; and
determining the presence of methylation at the locus by comparing the number of intact copies of the locus in the third and fourth portions to the number of total intact copies of the locus and/or intact methylated copies of the locus and/or intact unmethylated copies of the locus.

56. The method of claim 1, wherein the presence of methylation at the locus is compared between at least two nucleic acid samples.

57. The method of claim 56, wherein the at least two nucleic acid samples are isolated from at least two organisms having the same phenotype.

58. The method of claim 56, wherein the at least two nucleic acid samples are isolated from at least two organisms having different phenotypes.

59. The method of claim 56, comprising quantifying the intact methylated copies of the locus in a first sample and a second sample; and
comparing the quantity of amplified products from the two samples, thereby determining relative methylation at the locus between the two samples.

60. The method of claim 56, wherein a first nucleic acid sample is isolated from a cell suspected of being a cancer cell and a second nucleic acid sample is isolated from a non-cancerous cell.

61. The method of claim 1, wherein the presence of methylation at two or more loci is determined by
quantifying copies of intact DNA at the two different loci from a first portion contacted with a methylation-dependent restriction enzyme;
quantifying the intact DNA at the two loci from a second portion contacted with a methylation-sensitive restriction enzyme; and
comparing the quantities of the amplified products for the two loci.

62. The method of claim 1, wherein the population of nucleic acids is isolated from a cell.

63. The method of claim 62, wherein the cell is a member selected from the group consisting of: a plant cell, a fungal cell, a prokaryotic cell, an animal cell, a mammalian cell, and a cancer cell.

64. The method of claim 1, wherein the population of nucleic acids is isolated from a sample from a subject, wherein the sample is a member selected from the group consisting of: a body fluid and a secretion.

65. The method of claim 64, wherein the subject is a human.

66. The method of claim 65, wherein the subject is suspected of having cancer.

67. The method of claim 1, wherein the population of nucleic acids is isolated from a tissue biopsy from a subject.

68. The method of claim 67, wherein the subject is a human.

69. The method of claim 67, wherein the subject is suspected of having cancer.

70. The method of claim 67, wherein the locus comprises a sequence that is more methylated in diseased cells than in non-diseased cells.

71. The method of claim 67, wherein the locus comprises a sequence that is less methylated in diseased cells than in non-diseased cells.

72. The method of claim 1, wherein the quantifying step comprises a quantitative polymerase chain reaction (PCR).

73. The method of claim 72, wherein the quantitative amplification product is detected by detection of a label intercalated between bases of double stranded DNA sequences.

74. The method of claim 72, wherein the quantitative amplification product is detected by detecting hybridization of a detectably labeled oligonucleotide to the amplification product.

75. The method of claim 74, wherein the detectably labeled oligonucleotide is a labeled oligonucleotide probe comprising a fluorophore and a hairpin structure.

76. The method of claim 74, wherein the detectably labeled oligonucleotide is a dual labeled oligonucleotide probe comprising a pair of interactive labels.

77. The method of claim 76, wherein the pair of interactive labels are a quencher and a fluorophore.

78. The method of claim 76, wherein the fluorophore is activated to generate a detectable signal when the probe hybridizes to its target nucleic acid sequence.

79. The method of claim 76, wherein the fluorophore is activated to generate a detectable signal when the probe hybridizes to its target nucleic acid sequence and an enzyme with 5′ exonuclease activity cleaves the portion of the probe comprising the quencher.

80. The method of claim 1, further comprising adding sequence tags onto the ends of a population of nucleic acids before dividing the population of nucleic acids into equal portions, wherein,
step (c) comprises quantifying the remaining intact methylated copies of the locus in the first portion with primers that initiate amplification from the sequence tags; and
step (e) comprises quantifying the remaining unmethylated intact copies of the locus in the second portion with primers that initiate amplification from the sequence tags.

81. The method of claim 1, wherein the first portion is not digested with a methylation-dependent restriction enzyme and the second portion is not digested with a methylation-sensitive restriction enzyme.

82. The method of claim 1, wherein the quantitative amplification in steps (b) and (d) are monitored in real time.

83. The method of claim 1, wherein the quantitative amplification in steps (b) and (d) comprise quantitative PCR.

84. The method of claim 1, wherein the quantitative PCR comprises determining a cycle threshold.