# Patent

## Title
Targeted 2′-O-methylation of telomerase non-coding RNA

## Abstract

Processes and C/D box small nucleolar RNAs (snoRNAs) for altering telomerase activity and altering telomerase length are described. The processes of the invention involve the use of C/D box snoRNAs for targeted 2′-O-methylation modification of nucleotides in a pseudoknot region of the telomerase RNA. Depending on their position, the 2′-O-methylation modifications can cause an increase in telomerase activity and subsequent telomere lengthening or a decrease in telomerase activity and subsequent telomere shortening.

## Background
STATEMENT OF GOVERNMENT SUPPORT
This invention was made with U.S. Government support under grant number GM62937, awarded by the National Institutes of Health. The U.S. Government has certain rights in this invention.


REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY
The content of the electronically submitted sequence listing (Name: 2973.0010001_SeqListing_Updated; Size: 125,052 bytes; and Date of Creation: May 20, 2015) filed with the application is incorporated herein by reference in its entirety.
FIELD OF THE INVENTION
The invention relates generally to methods for causing a 2′-O-methylation modification of a nucleotide in the telomerase RNA by contacting the telomerase RNA with a C/D snoRNA engineered to guide the 2′-O-methylation modification. The invention further relates generally to methods for modulating telomerase activity through 2′-O-methylation modification of a nucleotide in the telomerase RNA by contacting the telomerase RNA component with a C/D snoRNA engineered to guide the 2′-O-methylation modification. The invention further relates to engineered C/D box snoRNA molecules that may direct such modifications.
BACKGROUND OF THE INVENTION
In eukaryotic cells, chromosomal ends are capped by telomeres, which are long tandem-repeat sequences complexed with proteins (Blackburn, E. H., et al., Nat. Med. 12:1133-8 (2006); Szostak, J. W., et al., Cell 29:245-55 (1982)). Telomeres maintain the integrity and stability of chromosomes, which would otherwise undergo incomplete replication, fusion or degradation with each cell division (Cech, T. R., Cell 116:273-9 (2004); Collins, K., Nat. Rev. Mol. Cell. Biol. 7:484-94 (2006)). Telomerase is responsible for telomere elongation and maintenance of chromosomal ends in most eukaryotes (Blackburn, E. H., et al., Nat. Med. 12:1133-8 (2006); Greider, C. W., et al., Cell 43:405-13 (1985)). It has long been known that telomerase is fundamental to cell survival, growth and death (Blasco, M. A., Nat. Chem. Biol. 3:640-9 (2007)). Telomere shortening is associated with ageing and telomerase malfunction is often associated with disease. For instance, most cancer cells have an unusually high level of telomerase activity (Kim, N. W., et al., Science 266:2011-5 (1994)). On the other hand, mutations in telomerase components have been linked to several degenerative diseases such as dyskeratosis congenita and aplastic anemia (Blasco, M. A., Nat. Chem. Biol. 3:640-9 (2007)). Thus, to understand the molecular mechanisms of these diseases and to identify new treatments, it is desirable to regulate telomerase activity in vivo.
Telomerase is a ribonucleoprotein (RNP) complex (Greider, C. W., et al., Nature 337:331-7 (1989)) that consists of one noncoding RNA (known as TERC or TR in humans and TLC1 in Saccharomyces cerevisiae) (Singer, M. S., et al., Science 266:404-9 (1994)) and several proteins, including a reverse transcriptase (TERT in humans and Est2p in Saccharomyces cerevisiae) (Lingner, J., et al., Science 276:561-7 (1997)). The telomerase non-coding RNA not only folds into a structure that tethers proteins but also serves as a template for reverse transcription (Zappulla, D. C., et al., Proc. Natl. Acad. Sci. USA 101:10024-9 (2004)), which leads to the addition of a specific repeated sequence to the chromosome ends. S. cerevisiae TLC1 and its homologs in other organisms (including mammals) have been extensively studied. Several other possible functions (including catalysis) of telomerase RNA have been proposed (Miller, M. C., et al., Proc. Natl. Acad. Sci. USA 99:6585-90 (2002); Qiao, F., et al., Nat. Struct. Mol. Biol. 15:634-40 (2008)). Furthermore, NMR studies and computational modeling coupled with functional analysis have revealed a conserved triple-helix structure within the pseudoknot region of human and K. lactis telomerase RNAs (Shefer, K., et al., Mol. Cell. Biol. 27:2130-43 (2007); Theimer, C. A., et al., Mol. Cell. 17:671-82 (2005)). Recently, Qiao, et al. has presented experimental evidence for the presence of a similar triple-helix structure in yeast TLC1 RNA (Qiao, F., et al., Nat. Struct. Mol. Biol. 15:634-40 (2008)) (FIG. 1A). Changes of 2′-OH groups of nucleotides in and adjacent to the triple-helix region to 2′-H or 2′-OMe (2′-O-methylated) lead to reduction of telomerase activity in yeast and mammalian in vitro systems (Qiao, F., et al., Nat. Struct. Mol. Biol. 15:634-40 (2008)).
Box C/D ribonucleoproteins (RNPs) are modifying enzymes that introduce 2′-O-methylation into rRNAs and snRNAs at specific sites (Yu, Y. T., et al., in H. Grosjean (Ed.): Fine-Tuning of RNA Functions by Modification and Editing, vol. 12, Springer-Verlag, Berlin Heidelberg (2005)). Box C/D RNPs comprise one small RNA (box C/D RNA) and four core proteins (Fibrillarin or Nop1p in S. cerevisiae, 15.5-kDa protein, Nop56 and Nop58) (Yu, Y. T., et al., in H. Grosjean (Ed.): Fine-Tuning of RNA Functions by Modification and Editing, vol. 12, Springer-Verlag, Berlin Heidelberg (2005)). A typical box C/D RNA folds into a unique secondary structure, leaving two short sequences—one between box C and box D′ and one between box C′ and box D—unpaired or single stranded (FIG. 1B). These single-stranded sequences function as guides that base-pair with the natural rRNA and snRNA substrates, thereby directing 2′-O-methylation at specific sites (Bachellerie, J. P., et al., Trends Biochem. Sci. 20:261-4 (1995); Cavaille, J., M. et al., Nature 383:732-5 (1996); Kiss-Laszlo, Z., et al., Cell 85:1077-88 (1996)). Without exception, 2′-O-methylation occurs at the target nucleotide in the substrate RNA that is base-paired to the nucleotide in snoRNA precisely 5 nucleotides upstream from box D (or D′; FIG. 1B) (Cavaille, J., M. et al., Nature 383:732-5 (1996); Kiss-Laszlo, Z., et al., Cell 85:1077-88 (1996)). Once the box C/D snoRNA finds its nucleotide target, fibrillarin, a methyl transferase associated with the box C/D guide RNA, delivers the methyl group to the target nucleotide at the 2′-O position. The “Box D+5 rule” for predicting the site of 2′-O-methylation guided by box C/D RNAs has been verified in various organisms including yeast, Xenopus and human, suggesting that RNA-guided 2′-O-methylation of rRNA and snRNA is universal among eukaryotes (Kiss, T. et al., Embo J 20:3617-22 (2001); Kiss, T., et al., Cell 109:145-8 (2001); Peculis, B., Curr. Biol. 7:R480-2 (1997); Smith, C. M., et al., Cell 89:669-72 (1997)). Given the detailed mechanism of RNA-guided RNA 2′-O-methylation, it is possible to design artificial box C/D RNAs to target telomerase RNA in and adjacent to the triple-helix region, thus offering an opportunity to manipulate telomerase activity in vivo.
As disclosed in detail herein, the present inventors show that artificial box C/D RNAs can target 2′-O-methylation at specific sites in and adjacent to the triple-helix structure of telomerase, thereby affecting telomerase activity in vivo. 2′-O-methylation did not affect the steady-state level of TLC1, and 2′-O-methylated TLC1 was incorporated into telomerase RNP. Thus, these results indicate that telomerase activity can be manipulated in vivo.
SUMMARY OF THE INVENTION
The invention is directed to method for causing the 2′-O-methylation of a nucleotide at a specific position of a telomerase RNA by contacting the telomerase RNA with a C/D box snoRNA that causes 2′-O-methylation at the specific position in the telomerase RNA. The method may be performed in vivo. In certain embodiments, the method of the invention further entails assembling the modified telomerase RNA into a telomerase ribonucleoprotein complex.
In certain embodiments, the telomerase RNA is human telomerase RNA encoded by a nucleic acid comprising SEQ ID NO: 266. In certain embodiments, the C/D box snoRNA is encoded by a nucleic acid comprising a sequence selected from: SEQ ID NOs:300-314.
The invention is also directed to a method for altering telomerase enzymatic activity by providing a telomerase RNA and contacting the telomerase RNA component with a C/D box snoRNA that causes a 2′-O-methylation modification of a nucleotide in the telomerase RNA. In certain embodiments, the nucleotide that is 2′-O-methylated is located in the pseudoknot region of the telomerase RNA. The 2′-O-methylation modification of a nucleotide in the telomerase RNA alters the telomerase enzymatic activity, e.g., the modification may either increase or decrease telomerase activity.
The invention is also directed to a method for altering telomere length comprising providing a cell expressing telomerase with a telomerase RNA having and providing a nucleic acid encoding a C/D box snoRNA that causes a 2′-O-methylation modification of a nucleotide in the telomerase RNA in a manner that cause the guide RNA to be expressed in the cell. In certain embodiments, the nucleotide that is 2′-O-methyled is located in the pseudoknot region of the telomerase RNA. The 2′-O-methylation modification of a nucleotide in the telomerase RNA alters the length of telomeres in the cell, e.g., the modification may either increase or decrease telomere length.
The present invention is also directed to engineered C/D box snoRNA molecules that allow for targeted modification of the telomerase RNA. In certain embodiments, the invention is directed to nucleic acids encoding an engineered C/D box snoRNA, wherein the nucleic acid encodes a sequence comprising nucleic acids selected from SEQ ID NOs:300-314.



DESCRIPTION OF THE FIGURES
FIG. 1 shows schematic diagrams of the yeast telomerase RNA and a yeast Box C/D RNA. (A) The pseudoknot structure of S. cerevisiae TLC1 RNA is shown schematically (modified from (Qiao, F., et al., Nat. Struct. Mol. Biol. 15:634-40 (2008))). Shaded nucleotides and dotted lines denote the triple helix. The template sequence is also indicated. Nucleotides in the triple-helix region that were evaluated in the current work are numbered. (B) The box C/D RNA structure is shown schematically. Boxes C, D′, C′ and D are indicated. The sequence between box C and box D′ and the sequence between box C′ and box D function as guides that base-pair with target RNA (thick line), as shown. 2′OMe denotes the target nucleotide to be 2′-O-methylated. The two nucleotide sequences shown in FIG. 1A represent nucleotides 751-765 and 797-814 of SEQ ID NO: 282.
FIG. 2 shows experimental results demonstrating that Artificial box C/D guide RNAs are expressed and functional. (A) Northern blot assay for gRNA expression. Total RNA isolated from cells (yCH-001) expressing no gRNA (empty vector) (lane 1), a random (control) gRNA (lanes 2), gRNA-A804 (lane 3), gRNA-A805 (lane 4), gRNA-A806 (lane 5), gRNA-U809 (lane 6), gRNA-A810 (lane 7), or gRNA-U811 (lane 8) was used for Northern blot analysis. Probes for U1 (loading control) and gRNAs were used, and signals corresponding to these RNAs are indicated. The levels of some gRNAs are slightly lower than the others, but they were all estimated (based on northern blotting) to be higher than the endogenous naturally-occurring box C/D RNAs tested (data not shown). (B) 2′-O-methylation mapping of individually modified nucleotides. Total RNA isolated from cells (yCH-002) expressing a random gRNA (control; lanes 1 and 2), gRNA-A804 (lanes 3 and 4), gRNA-A805 (lanes 5 and 6), gRNA-A806 (lanes 7 and 8), gRNA-U809 (lanes 9 and 10), gRNA-A810 (lanes 11 and 12) or gRNA-U811 (lanes 13 and 14) was used for primer-extension analysis in the presence of high (H; 1 mM, odd-numbered lanes) or low (L; 0.001 mM, even-numbered lanes) dNTP concentrations. Arrows indicate the stop/pause signals corresponding to the 2′-O-methylated residues. The TLC1 sequencing ladder is shown on the left. (C) The strategy behind ligation-based 2′-O-methylation assay (also see Methods and text). The thick lines represent the target RNA substrate, and the thin lines stand for primer pairs (ND, non-discriminating; D, discriminating) used for ligation. N denotes a test nucleotide lacking 2′-O-methylation; Nm represents a test nucleotide that is 2′-O-methylated. Nicks (on the 5′ or 3′ side of the test nucleotide) are also shown. (D) Ligation-based quantification of 2′-O-methylation. RNA was isolated from cells after 30 generations that expressed a random (control) gRNA (lanes 1, 2, 5, 6, 9, 10, 13, 14, 17, 18, 21 and 22), gRNAA804 (lanes 3 and 4), gRNA-A805 (lanes 7 and 8), gRNA-A806 (lanes 11 and 12), gRNA-U809 (lanes 15 and 16), gRNA-A810 (lanes 19 and 20) or gRNA-U811 (lanes 23 and 24) and assayed for 2′-O-methylation at the respective positions with position specific primer pairs (A804, lanes 1-4; A805, lanes 5-8; A806, lanes 9-12; U809, lanes 13-16; A810, lanes 17-20; U811, lanes 21-24). D, discriminating primer pair (odd numbered lanes); N, non-discriminating primer pair (even-numbered lanes). In all lanes, an additional pair of labeled primers was also included for a loading control. The relative modification efficiencies are calculated and shown in parentheses. (E) As in (D) except that RNA was isolated from cells after 590 generations.
FIG. 3 shows experimental results demonstrating that 2%0-methylated TLC1 RNA is incorporated into telomerase RNP. (A) 2′-Omethylation has no effect on the steady-state level of TLC1 RNA. Cells expressing a random gRNA (control; lane 1), gRNA-A804 (lane 2), gRNA-A805 (lane 3), gRNA-A806 (lane 4), gRNA-U809 (lane 5), gRNA-A810 (lane 6) or gRNA-U811 (lane 7), were grown for 30 generations (top panel), 310 generations (middle panel), and 590 generations (bottom panel). RNAs were isolated from these cells and analyzed by northern blotting with TLC1-specific and U1-specific probes. TLC1 RNA levels were calculated relative to U1 (in percentage). (B) Incorporation of TLC1 RNA into telomerase RNP. Extracts prepared from cells expressing a random gRNA (control; top panel) or gRNA-U809 were loaded on a 15-40% glycerol gradient. Nineteen fractions were collected. RNA from each fraction was analyzed by northern blotting with TLC1-specific and U1-specific probes. On the right is a plot showing the TLC1 and U1 signal peaks. (C) Fractions 12-15 of the gradient described in (B) were pooled, RNAs were recovered, and primer extension was carried out in the presence of high (H; lanes 1 and 3) or low (L; lanes 2 and 4) dNTP concentrations. Lanes 1 and 2 are from cells expressing a random gRNA (control), and lanes 3 and 4 are from cells expressing gRNA-U809. A TLC1 sequencing ladder was electrophoresed in parallel on the left. A signal corresponding to 2%0-methylated U809 is indicated. (D) Western and northern analyses of immunoprecipitated Est2p complex. A yeast strain, in which EST2 gene is fused with a protein A tag, was transformed with a plasmid containing no gRNA (lane 8), a random (control) gRNA (lane 1), gRNA-A804 (lane 2), gRNA-A805 (lane 3), gRNA-A806 (lane 4), gRNA-U809 (lane 5), gRNA-A810 (lane 6) or gRNA-U811 (lane 7). IgG precipitation was subsequently carried out. As a control, an untagged yeast strain was also used for IgG precipitation (lane 9). Precipitated proteins were recovered, and western analysis (with anti-protein A antibodies) performed. Furthermore, RNA co-precipitated with protein A-Est2p was recovered, and northern analysis carried out. Probes for U1 (loading control) and TLC1 were used, and signals corresponding to these RNAs are indicated. As a control, total cellular RNA was also used (lane 10). (E) 2′-O-methylation mapping was conducted as in (C). All seven samples [corresponding to lanes 1-7 in (D)] were assayed.
FIG. 4 shows the experimental results demonstrating of an in vitro telomerase activity assay. (A) IgG-bound (protein A-Est2p) fraction described in FIG. 3D was used directly for in vitro telomerase activity assay (Seto, A. G., et al., Rna 9:1323-32 (2003)). Three independent sets of experiments, each in duplicate, were carried out. Shown is one such experiment. Duplicate lanes represent two independent reactions for each strain. A control band [for recovery and loading control (Seto, A. G., et al., Nature 401:177-80 (1999))] is also shown. (B) Relative telomerase activity of the IgG-bound fraction, derived from each strain, was quantified based on three independent sets of duplicate experiments. The quantification was performed by comparing the intensity of the bands (the sum of all seven bands) in each lane. Adjustment was made for every band by deducting a background area immediately above the band. Percentage of in vitro telomerase activity of each strain was calculated against control activity (set to 100%). The error bars represent the standard deviation of the measurements. Asterisks (*) indicate that the P-values are less than 0.05 (calculated using the Microsoft Exel t-test software).
FIG. 5 shows Southern analysis of chromosome end length in cells expressing various artificial guide RNAs. Cells (yCH-002) expressing a random gRNA (control; lanes 1-6); gRNA-A804 (lanes 7-12); gRNA-A805 (lanes 13-18), gRNA-A806 (lanes 19-24), gRNA-U809 (lanes 25-32), gRNA-A810 (lanes 33-38) or gRNA-U811 (lanes 39-44), were harvested after growing for the indicated number of generations (G#). DNA was recovered, digested with XhoI and hybridized with two radiolabeled probes, a telomere-specific one and a chromosome IV-specific one (as an internal control). The fragment of chromosome IV (Chr4) and the telomeres (TRF) are indicated. For each strain, two independent experiments are presented in duplicate lanes. The distances between the signal peaks of Chr4 and TRF were measured using Imagequant software (Molecular Dynamics) (Bachellerie, J. P., et al., Trends Biochem. Sci. 20:261-4 (1995)). Shown in parentheses at the top of each strain are the relative changes in distance between two time points (30 and 590 generations) (difference in average distance between the two time points, divided by the average distance at 30 generations). “+” indicates telomere lengthening, and “−” indicates telomere shortening.
FIG. 6 shows the experimental results of a telomere position effect assay. (A) Cells (yCH-002) expressing a random gRNA (control), gRNA-A804, gRNA-A805, gRNA-A806, gRNA-U809, gRNA-A810 or gRNA-U811 were grown for the indicated number of generations and then plated on SD-Leu medium with or without 5-FOA. (B) DNAs were recovered from the cells described in (A), cleaved with PstI and hybridized with a URA3-specific radiolabeled probe and a chromosome IV—specific radiolabeled probe. Left panel: the schematic shows the modified chromosome VII with URA3 inserted near the telomere. A PstI site and the site of hybridization with the URA3 probe (a thick line with a star) are indicated. Right panel: the signals corresponding to the chromosome IV fragment and the telomere of chromosome VII are indicated.
FIG. 7 shows an alignment of a portion of the telomerase RNA from vertebrates showing part of the pseudoknot region of the telomerase RNA. The alignment is taken from the Telomerase Database (telomere.asu.edu: Podlevsky, J D., et al., Nucleic Acids Research 36 (database issue):D339-D343(2008)).



DETAILED DESCRIPTION
Definitions
Unless otherwise expressly defined, the terms used herein are to be understood according to their ordinary meaning in the art. Terms used in the singular or referred to as “a” or “an” also include the plural and vice versa, unless otherwise specified or indicated by context. Standard techniques and procedures are generally performed according to conventional methods in the art and various general references (see generally, Sambrook et al. Molecular Cloning: A Laboratory Manual, 2nd ed. (1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., which is incorporated herein by reference), which are provided throughout this document. The disclosures of the references cited in this document are all incorporated herein by reference.
As used herein, the term “Small nucleolar RNAs (snoRNAs)” refers to a class of small non-coding RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. There are two main classes of snoRNA, the C/D box snoRNAs which are associated with methylation modifications and H/ACA box snoRNAs which are associated with pseudouridylation modifications. snoRNAs may be represented herein as a RNA nucleic acid sequence or as a DNA nucleic acid sequence encoding the RNA nucleic acid sequence.
As used herein, the term “guide sequence” refers to a nucleic acid sequence of a snoRNA which base pairs with a target RNA molecule to guide modification of the target molecule.
As used herein, the term “engineered snoRNA” refers to a RNA for which part of the native sequence has been modified. In certain examples, engineered snoRNAs have the native guide sequence replaced with an engineered guide sequence that causes the snoRNA to target RNA modification at a specific position in the target RNA.
As used herein, the term “target RNA” or “target RNA molecule” refers to any RNA in which a modification is effected by contacting the target RNA with a snoRNA.
As used herein, the term “telomerase ribonucleoprotein complex” refers to the enzymatically functional complex of telomerase ribonucleoproteins and telomerase RNA.
As used herein, the term “telomerase RNA” or “telomerase RNA component” refers to the non-coding RNA molecule that is present in the telomerase ribonucleoprotein complex.
As used herein, the terms “altering,” “modulating,” or “modifying,” as they relate to telomerase activity, refer to a difference in the enzymatic activity of the telomerase ribonucleoprotein complex containing a modified telomerase RNA, e.g., a telomerase ribonucleotprotein complex containing telomerase RNA having a modified nucleotide that is not present in the native telomerase RNA, when compared with the enzymatic activity of a native (wild type) telomerase, e.g., a telomerase ribonucleoprotein complex containing native telomerase RNA. A telomerase ribonucleoprotein may have increased or decreased enzymatic activity compared to wild type within the meaning of this term.
The present invention provides methods and C/D box small nucleolar RNAs (snoRNAs), or guide RNAs, that allow for the alteration of telomerase enzymatic activity and, subsequently, telomerase length. The methods of the present invention involve targeting the 2′-O-methylation modification of nucleotides in a pseudoknot region of the telomerase RNA, see, e.g., (FIG. 1A).
As is exemplified herein, 2′-O-methylation of nucleotides in a pseudoknot region of the telomerase RNA results in changes in telomere length. In certain embodiments, modification of a nucleotide at a specific position in the telomerase RNA causes reduced or decreased telomerase activity, resulting in telomere shortening. In other embodiments, modification of a nucleotide at a specific position in the telomerase RNA causes increased telomerase activity, resulting in telomere lengthening.
The present invention contemplates the use of C/D box snoRNAs for the targeted 2′-O-methylation of the telomerase RNA component. C/D box snoRNAs are known in the art. It is known that target RNA 2′-O-methylation always occurs in the residue base-paired to the nucleotide in snoRNA precisely 5 nucleotides upstream from box D (or D′) (FIG. 1B) (Kiss-Laszlo, Z., et al., Cell 85:1077-88 (1996); Balakin, et al., Cell 86:823-34 (1996); Cavaille, J., M. et al., Nature 383:732-5 (1996)). Once the box C/D snoRNA finds its nucleotide target, fibrillarin, a methyl-transferase associated with the box C/D guide RNA, delivers the methyl group to the target nucleotide at the 2′-O position. The “Box D+5 rule” for predicting the site of 2′-O-methylation guided by snoRNAs has since been confirmed in various organisms including yeast, Xenopus and human (Smith, C. M., et al., Cell 89:669-72 (1997); Peculis, B., Curr. Biol. 7:R480-2 (1997); Kiss, T. et al., Embo J 20:3617-22 (2001); Kiss, T., et al., Cell 109:145-8 (2001)). Most Box D or D′ sequences are CUGA while some less conserved Box D or D′ sequences may be AUGA as is well known to a person of skill in the art.
The present invention provides a novel, improved way to regulate telomerase activity. Over the years, a number of different strategies have been developed for up- or down-regulating telomerase activity in various organisms. Among them, the antisense RNA approach and RNA interference (RNAi) to regulate mammalian telomerase activity have drawn a great deal of attention. Although well conceptualized, the antisense RNA approach is effective for only a few cases, and most trials have failed for a number of reasons.
One of the most important reasons for the failure of antisense RNA trials is the instable nature of a foreign antisense RNA when introduced into cells. Usually, the antisense RNA is significantly degraded before reaching its target. The development of RNAi strategies has changed the way gene silencing can be achieved. Using the RNAi strategies, several labs have knocked down telomerase RNA, the protein components of telomerase RNP, or proteins that are relevant to telomerase function, thus inhibiting telomerase activity (Wang, Y., et al., Cancer Biol. Ther. 7(6):896-901 (2008); Chen, S. M., et al., Cancer Biol. Ther. 7(5):734-739 (2008); Kosciolek, B. A., et al., Mol. Cancer. Ther. 2(3):209-16 (2003); Li, S., et al., Cancer Res. 64(14):4833-40 (2004); Patry, C., et al., Cancer Res 63(22):7679-88 (2003); Coussens, M., et al., Proc. Natl. Acad. Sci. USA 107 (31): p. 13842-7 (2010)). In some cases, knockdown of proteins that negatively impact telomerase function (e.g., those that block telomerase recruitment to telomeres or suppress hTERT expression) can upregulate telomerase activity (Maurelli, R., et al., FASEB J 20(9):1516-8 (2006); Bazarov, A. V., et al., Aging Cell 9(5):736-46 (2010)). However, although convenient and widely used, the RNAi approach also has some limitations. For instance, the knock down of a gene usually requires many trials with different siRNAs—there are no exact rules for siRNA design. With regard to genes for which RNAi has an effect, they are usually just moderately “knocked down”. In at least some organisms reported (e.g., C. elegans), the RNAi effect is less specific, probably due to transitive RNAi by a secondary siRNA (Sijen, T., et al., Cell 107(4):465-76 (2001)).
In comparison, the use of RNA-guided modifications targeted to telomerase RNA is advantageous in many different ways. First, RNA-guided RNA modification is absolutely conserved across species, from yeast to humans (Yu, Y. T., et al., in H. Grosjean (Ed.): Fine-Tuning of RNA Functions by Modification and Editing, vol. 12, Springer-Verlag, Berlin Heidelberg (2005)). Thus, this approach is, in principle, applicable to all eukaryotes. Second, guide RNAs are stable in cells (Balakin, et al., Cell 86:823-34 (1996)); Tycowski, K. T., et al., Nature 379(6564):464-6 (1996)). Just as their native counterparts, foreign guide RNAs, when introduced into cells, they are assembled into RNA-protein complexes that are stable presumably throughout the lifetime of cells, and possibly are even passed on to subsequent generations. Third, there are simple and clear rules for guide RNA design (Huang, C. et al., Mol. Cell. Biol. 30(18):4368-78 (2010). To target different sites within telomerase RNA for modification, only the guide sequence of a guide RNA needs to be changed accordingly. Fourth, as shown in the examples below, modification is highly efficient—for a given site more than 70% of modification was observed. Fifth, based on a large amount of experimental evidence and experience (Huang, C. et al., Mol. Cell. Biol. 30(18):4368-78 (2010); Zhao, X. et al., Nat. Methods 5 (1): p. 95-100 (2008)). RNA-guided nucleotide 2′-O-methylation is extremely site-specific. Indeed, modification occurs only in the target site in telomerase RNA or in other RNA. Sixth, as shown in the examples below, depending on the sites to which 2′-O-methylation is targeted, telomerase activity can be either enhanced or inhibited, thus offering an opportunity to manipulate telomerase activity in both directions. Finally, targeted 2′-O-methylation also offers a unique opportunity to investigate the functionality of the RNA backbone (particularly, 2′-OH moieties) (Huang, C. et al., Mol. Cell. Biol. 30(18):4368-78 (2010); Zhao, X. et al., Nat. Methods 5 (1): p. 95-100 (2008)), which has proved to be difficult to study in vivo (mutation of the 2′-OH at the DNA level is impossible).
snoRNAs
For the guided modification mechanisms of the present invention, the snoRNA guide sequences can be modified to base pair with a sequence of the target telomerase RNA adjacent to the nucleotide to be modified. The engineered snoRNA guide sequences should be made to base pair with the appropriate sequence in the target RNA so that the nucleotide is in the proper position to undergo modification.
The present invention contemplates the use of C/D box snoRNAs engineered to effect a 2′-O-methylation modification at a specific position of the subject telomere RNA. C/D box RNAs vary across species, but all allow for 2′-O-modification at the “Box D+5” position. Therefore, C/D box snoRNAs from various species may be targeted to a specific residue by placing a guide sequence upstream of Box D of the snoRNA so that the residue to be modified is 5 nucleotides upstream from Box D. For example, in the case of most snoRNAs, the residue to be modified is 5 nucleotides upstream from the C of the CUGA Box D sequence. With this method, almost any C/D box snoRNA may be engineered to effect 2-O-methyl modification of a selected base in a target telomerase RNA.
One of skill in the art will recognize that almost any human C/D box snoRNA may be used in the present invention. Examples of nucleic acids encoding human C/D box snoRNAs that may be modified for use with the present invention, named according to the HUGO Gene Nomenclature Committee convention, include: SNORD 14A (SEQ ID NO: 1), SNORD 14B (SEQ ID NO: 2), SNORD 15A (SEQ ID NO: 3), SNORD 15B (SEQ ID NO: 4), SNORD 16 (SEQ ID NO: 5), SNORD 17 (SEQ ID NO: 6), SNORD 18A (SEQ ID NO: 7), SNORD 18B (SEQ ID NO: 8), SNORD 18C (SEQ ID NO: 9), SNORD 19 (SEQ ID NO: 10), SNORD 19B (SEQ ID NO: 11), SNORD 20 (SEQ ID NO: 12), SNORD 21 (SEQ ID NO: 13), SNORD 22 (SEQ ID NO: 14), SNORD 23 (SEQ ID NO: 15), SNORD 24 (SEQ ID NO: 16), SNORD 25 (SEQ ID NO: 17), SNORD 26 (SEQ ID NO: 18), SNORD 27 (SEQ ID NO: 19), SNORD 28 (SEQ ID NO: 20), SNORD 29 (SEQ ID NO: 21), SNORD 30 (SEQ ID NO: 22), SNORD 31 (SEQ ID NO: 23), SNORD 32A (SEQ ID NO: 24), SNORD 32B (SEQ ID NO: 25), SNORD 34 (SEQ ID NO: 26), SNORD 35A (SEQ ID NO: 27), SNORD 35B (SEQ ID NO: 28), SNORD 36A (SEQ ID NO: 29), SNORD 36B (SEQ ID NO: 30), SNORD 36C (SEQ ID NO: 31), SNORD 37 (SEQ ID NO: 32), SNORD 38A (SEQ ID NO: 33), SNORD 38B (SEQ ID NO: 34), SNORD 41 (SEQ ID NO: 35), SNORD 42A (SEQ ID NO: 36), SNORD 42B (SEQ ID NO: 37), SNORD 43 (SEQ ID NO: 38), SNORD 44 (SEQ ID NO: 39), SNORD 45A (SEQ ID NO: 40), SNORD 45B (SEQ ID NO: 41), SNORD 45C (SEQ ID NO: 42), SNORD 46 (SEQ ID NO: 43), SNORD 47 (SEQ ID NO: 44), SNORD 48 (SEQ ID NO: 45), SNORD 49A (SEQ ID NO: 46), SNORD 49B (SEQ ID NO: 47), SNORD 50 (SEQ ID NO: 48), SNORD 50B (SEQ ID NO: 49), SNORD 51 (SEQ ID NO: 50), SNORD 52 (SEQ ID NO: 51), SNORD 53 (SEQ ID NO: 52), SNORD 54 (SEQ ID NO: 53), SNORD 56 (SEQ ID NO: 54), SNORD 57 (SEQ ID NO: 55), SNORD 58A (SEQ ID NO: 56), SNORD 58B (SEQ ID NO: 57), SNORD 58C (SEQ ID NO: 58), SNORD 59A (SEQ ID NO: 59), SNORD 59B (SEQ ID NO: 60), SNORD 60 (SEQ ID NO: 61), SNORD 61 (SEQ ID NO: 62), SNORD 62A (SEQ ID NO: 63), SNORD 62B (SEQ ID NO: 64), SNORD 63 (SEQ ID NO: 65), SNORD 64 (SEQ ID NO: 66), SNORD 65 (SEQ ID NO: 67), SNORD 66 (SEQ ID NO: 68), SNORD 67 (SEQ ID NO: 69), SNORD 69 (SEQ ID NO: 70), SNORD 70 (SEQ ID NO: 71), SNORD 71 (SEQ ID NO: 72), SNORD 72 (SEQ ID NO: 73), SNORD 73A (SEQ ID NO: 74), SNORD 73B (SEQ ID NO: 75), SNORD 74 (SEQ ID NO: 76), SNORD 75 (SEQ ID NO: 77), SNORD 76 (SEQ ID NO: 78), SNORD 77 (SEQ ID NO: 79), SNORD 78 (SEQ ID NO: 80), SNORD 79 (SEQ ID NO: 81), SNORD 80 (SEQ ID NO: 82), SNORD 81 (SEQ ID NO: 83), SNORD 82 (SEQ ID NO: 84), SNORD 83A (SEQ ID NO: 85), SNORD 83A (SEQ ID NO: 86), SNORD 84 (SEQ ID NO: 87), SNORD 85 (SEQ ID NO: 88), SNORD 86 (SEQ ID NO: 89), SNORD 87 (SEQ ID NO: 90), SNORD 88A (SEQ ID NO: 91), SNORD 88B (SEQ ID NO: 92), SNORD 88C (SEQ ID NO: 93), SNORD 89 (SEQ ID NO: 94), SNORD 90 (SEQ ID NO: 95), SNORD91A (SEQ ID NO: 96), SNORD91B (SEQ ID NO: 97), SNORD 92 (SEQ ID NO: 98), SNORD 93 (SEQ ID NO: 99), SNORD 94 (SEQ ID NO: 100), SNORD 95 (SEQ ID NO: 101), SNORD 96A (SEQ ID NO: 102), SNORD 96B (SEQ ID NO: 103), SNORD 97 (SEQ ID NO: 104), SNORD 98 (SEQ ID NO: 105), SNORD 99 (SEQ ID NO: 106), SNORD 100 (SEQ ID NO: 107), SNORD 101 (SEQ ID NO: 108), SNORD 102 (SEQ ID NO: 109), SNORD 103A (SEQ ID NO: 110), SNORD 103B (SEQ ID NO: 111), SNORD 104 (SEQ ID NO: 112), SNORD 105A (SEQ ID NO: 113), SNORD 105B (SEQ ID NO: 114), SNORD 107 (SEQ ID NO: 115), SNORD 108 (SEQ ID NO: 116), SNORD 109A (SEQ ID NO: 117), SNORD 109B (SEQ ID NO: 118), SNORD 110 (SEQ ID NO: 119), SNORD 111A (SEQ ID NO: 120), SNORD 111B (SEQ ID NO: 121), SNORD 112 (SEQ ID NO: 122), SNORD 113-1 (SEQ ID NO: 123), SNORD 113-2 (SEQ ID NO: 124), SNORD 113-3 (SEQ ID NO: 125), SNORD 113-4 (SEQ ID NO: 126), SNORD 113-5 (SEQ ID NO: 127), SNORD 113-6 (SEQ ID NO: 128), SNORD 113-7 (SEQ ID NO: 129), SNORD 113-8 (SEQ ID NO: 130), SNORD 113-9 (SEQ ID NO: 131), SNORD 114-1 (SEQ ID NO: 132), SNORD 114-2 (SEQ ID NO: 133), SNORD 114-3 (SEQ ID NO: 134), SNORD 114-4 (SEQ ID NO: 135), SNORD 114-5 (SEQ ID NO: 136), SNORD 114-6 (SEQ ID NO: 137), SNORD 114-7 (SEQ ID NO: 138), SNORD 114-8 (SEQ ID NO: 139), SNORD 114-9 (SEQ ID NO: 140), SNORD 114-10 (SEQ ID NO: 141), SNORD 114-11 (SEQ ID NO: 142), SNORD 114-12 (SEQ ID NO: 143), SNORD 114-13 (SEQ ID NO: 144), SNORD 114-14 (SEQ ID NO: 145), SNORD 114-15 (SEQ ID NO: 146), SNORD 114-16 (SEQ ID NO: 147), SNORD 114-17 (SEQ ID NO: 148), SNORD 114-18 (SEQ ID NO: 149), SNORD 114-19 (SEQ ID NO: 150), SNORD 114-20 (SEQ ID NO: 151), SNORD 114-21 (SEQ ID NO: 152), SNORD 114-22 (SEQ ID NO: 153), SNORD 114-23 (SEQ ID NO: 154), SNORD 114-24 (SEQ ID NO: 155), SNORD 114-25 (SEQ ID NO: 156), SNORD 114-26 (SEQ ID NO: 157), SNORD 114-27 (SEQ ID NO: 158), SNORD 114-28 (SEQ ID NO: 159), SNORD 114-29 (SEQ ID NO: 160), SNORD 114-30 (SEQ ID NO: 161), SNORD 114-31 (SEQ ID NO: 162), SNORD 116-1 (SEQ ID NO: 163), SNORD 116-2 (SEQ ID NO: 164), SNORD 116-3 (SEQ ID NO: 165), SNORD 116-4 (SEQ ID NO: 166), SNORD 116-5 (SEQ ID NO: 167), SNORD 116-7 (SEQ ID NO: 168), SNORD 116-8 (SEQ ID NO: 169), SNORD 116-9 (SEQ ID NO: 170), SNORD 116-10 (SEQ ID NO: 171), SNORD 116-11 (SEQ ID NO: 172), SNORD 116-12 (SEQ ID NO: 173), SNORD 116-13 (SEQ ID NO: 174), SNORD 116-14 (SEQ ID NO: 175), SNORD 116-15 (SEQ ID NO: 176), SNORD 116-16 (SEQ ID NO: 177). SNORD 116-17 (SEQ ID NO: 178), SNORD 116-18 (SEQ ID NO: 179), SNORD 116-19 (SEQ ID NO: 180), SNORD 116-20 (SEQ ID NO: 181), SNORD 116-21 (SEQ ID NO: 182), SNORD 116-22 (SEQ ID NO: 183), SNORD 116-23 (SEQ ID NO: 184), SNORD 116-24 (SEQ ID NO: 185), SNORD 116-25 (SEQ ID NO: 186), SNORD 116-26 (SEQ ID NO: 187), SNORD 116-27 (SEQ ID NO: 188), SNORD 116-28 (SEQ ID NO: 189), SNORD 116-29 (SEQ ID NO: 190), SNORD 116-6 (SEQ ID NO: 191), SNORD 117 (SEQ ID NO: 192), SNORD 118 (SEQ ID NO: 193), SNORD 119 (SEQ ID NO: 194), SNORD 121A (SEQ ID NO: 195), SNORD 121B (SEQ ID NO: 196), SNORD 123 (SEQ ID NO: 197), SNORD 124 (SEQ ID NO: 198), SNORD 125 (SEQ ID NO: 199), SNORD 126 (SEQ ID NO: 200), SNORD 127 (SEQ ID NO: 201), SNORD 2 (SEQ ID NO: 202), SNORD 3 (SEQ ID NO: 203), SNORD 3-2 (SEQ ID NO: 2 (4), SNORD 3-2B (SEQ ID NO: 205), SNORD 3-3 (SEQ ID NO: 206), SNORD 3-4 (SEQ ID NO: 207), SNORD 4A (SEQ ID NO: 208), SNORD 4B (SEQ ID NO: 209), SNORD 5 (SEQ ID NO: 210), SNORD 6 (SEQ ID NO: 211), SNORD 7 (SEQ ID NO: 212), SNORD 8 (SEQ ID NO: 213), SNORD 9 (SEQ ID NO: 214), SNORD 10 (SEQ ID NO: 215), SNORD 11 (SEQ ID NO: 216), SNORD 12 (SEQ ID NO: 217), SNORD 12B (SEQ ID NO: 218), SNORD 12 (SEQ ID NO: 219), SNORD 13 (SEQ ID NO: 220), SNORD115-1 (SEQ ID NO: 366), SNORD115-2 (SEQ ID NO: 367), SNORD115-3 (SEQ ID NO: 368), SNORD115-4 (SEQ ID NO: 369), SNORD115-5 (SEQ ID NO: 370), SNORD115-6 (SEQ ID NO: 371), SNORD115-7 (SEQ ID NO: 372), SNORD115-8 (SEQ ID NO: 373), SNORD115-9 (SEQ ID NO: 374), SNORD115-10 (SEQ ID NO: 375), SNORD115-11 (SEQ ID NO: 376), SNORD115-12 (SEQ ID NO: 377), SNORD115-13 (SEQ ID NO: 378), SNORD115-14 (SEQ ID NO: 379), SNORD115-15 (SEQ ID NO: 380), SNORD115-16 (SEQ ID NO: 381), SNORD115-17 (SEQ ID NO: 382), SNORD115-18 (SEQ ID NO: 383), SNORD115-19 (SEQ ID NO: 384), SNORD115-20 (SEQ ID NO: 385), SNORD115-21 (SEQ ID NO: 386), SNORD115-22 (SEQ ID NO: 387), SNORD115-23 (SEQ ID NO: 388), SNORD115-25 (SEQ ID NO: 389), SNORD115-26 (SEQ ID NO: 390), SNORD115-29 (SEQ ID NO: 391), SNORD115-30 (SEQ ID NO: 392), SNORD115-31 (SEQ ID NO: 393), SNORD115-32 (SEQ ID NO: 394), SNORD115-33 (SEQ ID NO: 395), SNORD115-34 (SEQ ID NO: 396), SNORD115-35 (SEQ ID NO: 397), SNORD115-36 (SEQ ID NO: 398), SNORD115-37 (SEQ ID NO: 399), SNORD115-38 (SEQ ID NO: 400), SNORD115-39 (SEQ ID NO: 401), SNORD115-40 (SEQ ID NO: 402), SNORD115-41 (SEQ ID NO: 403), SNORD115-42 (SEQ ID NO: 404), SNORD115-43 (SEQ ID NO: 405), SNORD115-44 (SEQ ID NO: 406), SNORD115-48 (SEQ ID NO: 407), SNORD 33 (SEQ ID NO: 408), SNORD 55 (SEQ ID NO: 409), SNORD 68 (SEQ ID NO: 410), or analogues thereof, e.g., a nucleic acid or polynucleotide comprising an nucleic acid sequence at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a known snoRNA sequence.
More information on human C/D box snoRNAs may be found in the LMBE snoRNABase database, which is available at www-snorna.biotoul.fr (see, Lestrade, L., and Weber, M. J. Nucleic Acids Res. 34 (database issue): D158-162 (2006)), as well as other databases which are well known to a person of skill in the art, such as the rFam database (rfam.sanger.ac.uk; see, P. P. Gardner, et al., Nucleic Acids Res. doi: 10.1093/nar/gkq1129 (2011)). The snoRNABase lists the location of the D and/or D′ Box and the native guide sequences in each snoRNA, allowing for a person of skill in the art to easily locate the Box D+5 position and engineer a snoRNA for specific targeting of residues for 2′-O-methyl modification.
Many of the human C/D box snoRNAs listed above have homologs in other vertebrate species, which may also be engineered accord to the invention, including: Macaca mulatta (rhesus monkey), Sus scrofa (pig), Danio rerio (zebrafish), Loxodonta africana (African savanna elephant), Lama pacos (alpaca), Cavia porcellus (domestic guinea pig), Bos taurus (cattle), Canis lupus familiaris (dog), Pan troglodytes (chimpanzee), Pongo abelii (Sumatran orangutan), Gorilla gorilla gorilla (Western lowland gorilla), Gorilla gorilla (Western Gorilla), Equus caballus (horse), Tursiops truncatus (bottlenosed dolphin), Myotis lucifugus (little brown bat), Oryctolagus cuniculus (rabbit), Felis catus (domestic cat), Rattus norvegicus (Norway rat), Mus musculus (house mouse) and Xenopus laevis (African clawed frog). Additional snoRNAs contemplated include those from: Danio rerio (zebrafish); invertabrates: Ciona intestinalis (sea squirt), Ciona savignyi (sea squirt), Strongylocentrotus purpuratus (purple sea urchin), Gammarus pulex (freshwater shrimp), Drosophila melanogaster (fruit fly), Drosophila virilis (fly), Chironomus tentans (fly), Anopheles gambiae (African malaria mosquito), Sialis lutaria (alderfly), Apis mellifera (honey bee), Bombyx mori (domestic silkworm), Bombyx mandarina (wild silkworm), Papilio xuthus (butterfly), Hodotermopsis japonicus (termite), Periplaneta fuliginosa (dusky-brown cockroach), Tapinoma nigerrimum (ant), Manica yessensis (ant), Myrmecia sp. (ant); Nematodes: Ascaris lumbricoides (common roundworm), Ascaris suum (pig round worm), Parascaris univalens, Caenorhabditis elegans; Fungi: Schizosaccharomyces pombe (fission yeast), Saccharomyces cerevisiae (baker's yeast), Saccharomyces pastorianus (lager yeast), Saccharomyces kluyveri, Kluyveromyces lactis, Candida albicans, Pichia guilliermondii, Pichia stipites, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus niger and Neurospora crassa. It is also contemplated that analogs of such C/D box snoRNAs may be used such as nucleic acids comprising an nucleic acid sequence at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a known snoRNA sequence for each C/D box snoRNA listed above. Examples of such homologs may be found in the rFam database. As the Box D sequence is highly conserved among species and typically has the sequence CUGA or AUGA, a person of skill in the art can locate the D and/or D′ Box and the native guide sequences in homolog snoRNAs. This allows for a person of skill in the art to easily locate the Box D+5 position and engineer a snoRNA for specific targeting of residues for 2′-O-methyl modification.
Still further examples of C/D box snoRNAs known in the art include the Saccharomyces cerevisiae snoRNAs: U14 (SEQ ID NO: 221), U18 (SEQ ID NO: 222), U24 (SEQ ID NO: 223), snR4 (SEQ ID NO: 224), snR13 (SEQ ID NO: 225), snR38 (SEQ ID NO: 226), snR39 (SEQ ID NO: 227), snR39b (SEQ ID NO: 228), snR40 (SEQ ID NO: 229), snR41 (SEQ ID NO: 230), snR45 (SEQ ID NO: 231), snR47 (SEQ ID NO: 232), snR48 (SEQ ID NO: 233), snR50 (SEQ ID NO: 234), snR51 (SEQ ID NO: 235), snR52 (SEQ ID NO: 236), snR53 (SEQ ID NO: 237), snR54 (SEQ ID NO: 238), snR55 (SEQ ID NO: 239), snR56 (SEQ ID NO: 240), snR57 (SEQ ID NO: 241), snR58 (SEQ ID NO: 242), snR59 (SEQ ID NO: 243), snR60 (SEQ ID NO: 244), snR61 (SEQ ID NO: 245), snR62 (SEQ ID NO: 246), snR63 (SEQ ID NO: 247), snR64 (SEQ ID NO: 248), snR65 (SEQ ID NO: 249), snR66 (SEQ ID NO: 250), snR67 (SEQ ID NO: 251), snR68 (SEQ ID NO: 252), snR69 (SEQ ID NO: 253), snR70 (SEQ ID NO: 254), snR71 (SEQ ID NO 255), snR72 (SEQ ID NO: 256), snR73 (SEQ ID NO: 257), snR74 (SEQ ID NO: 258), snR75 (SEQ ID NO: 259), snR76 (SEQ ID NO: 260), snR77 (SEQ ID NO: 261), snR78 (SEQ ID NO: 262), snR79 (SEQ ID NO: 263), snR87 (SEQ ID NO 264), snR190 (SEQ ID NO: 265) or analogues thereof, e.g., a nucleic acid or polynucleotide comprising an nucleic acid sequence at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a known snoRNA sequence. Further information on the above listed snoRNAs and other C/D box snoRNAs can be found in the UMASS Amherst Yeast snoRNA database (people.biochem.umass.edu/sfournier/fournierlab/snornadb/main.php, see, D. Piekna-Przybylska, et al., Rna 13(3):305-12)(2007)).
Telomerase Target RNAs
The target RNA molecules of the present invention comprise a telomerase RNA, for example, TR (or TERC) in humans. Examples of nucleic acids encoding telomerase RNAs that are suitable targets for the present invention are listed in the Telomerase Database (telomerase.asu.edu, see, Podlevsky, J. D., et al., Nucleic Acids Res. 36 (database issue):D339-D343(2008)). Examples of nucleic acids encoding telomerase RNA that may be targeted in the present invention include: vertabrates: Homo sapiens (human) (SEQ ID NO: 266), Oryctolagus cuniculus (domestic rabbit) (SEQ ID NO: 267), Cavia porcellus (domestic guinea pig) (SEQ ID NO: 268), Cricetulus griseus (Chinese hamster) (SEQ ID NO: 269), Mus musculus (mouse) (SEQ ID NO: 270), Rattus norvegicus (Norway rat) (SEQ ID NO: 271), \ Felis catus (cat) (SEQ ID NO: 272), Bos taurus (cattle) (SEQ ID NO: 273), Sus scrofa (pig) (SEQ ID NO: 274), Equus caballus (domestic horse) (SEQ ID NO: 275), Elephas maximus (Asian elephant) (SEQ ID NO: 276), Gallus gallus (chicken) (SEQ ID NO: 277), Bombina japonica (toad) (SEQ ID NO: 278), Xenopus laevis (African clawed frog) (SEQ ID NO: 279), Danio rerio (zebrafish) (SEQ ID NO: 280); Fungi: Schizosaccharomyces pombe (fission yeast) (SEQ ID NO: 281), Saccharomyces cerevisiae (baker's yeast) (SEQ ID NO: 282), Saccharomyces pastorianus (lager yeast) (SEQ ID NO: 283). Candida albicans (SEQ ID NO: 284), or analogues thereof, e.g., a nucleic acid or polynucleotide comprising an nucleic acid sequence at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a known telomerase RNA sequence.
Telomerase RNA has a triple-helix as part of a pseudoknot structure that has been shown to be conserved and important to catalysis (Shefer, K., et al., Mol. Cell Biol. 27:2130-43(2007); Qiao, F., et al., Nat. Struct. Mol. Biol. 15:634-40(2008)). In certain embodiments, C/D box snoRNAs are engineered to effect 2′-O-methylation modification on a nucleotide in the pseudoknot region of the telomerase RNA. The structures and sequences for the telomerase RNAs of the present invention are available to one of skill in the art in the literature, for instance in the Telomerase Database (telomerase.asu.edu/structures.html). From review of the structure and sequence information, one of skill in the art will be able to engineer a C/D box snoRNA having a guide sequence that guides the 2′-O-methylation modification of the desired nucleotide, i.e., the nucleotide complementary to the C/D snoRNA nucleotide 5 bases upstream from the D or D box of the snoRNA.
For example, in certain embodiments, modifications to human telomerase RNA are made at one or more of positions 171-191 of SEQ ID NO: 266, which is a region near the pseudoknot of the telomerase RNA. This region is highly conserved among vertebrates, and typically has a sequence of five or more adenosine residues follow by the sequence UGUC or CGUC. An alignment of this region of the telomerase RNA, taken from the Telomerase Database, is shown in FIG. 7. From this alignment, a person of skill in the art would be able to determine which residues in the pseudoknot region may be modified according to the invention. For example, a person of skill in the art would recognized conserved sequences at positions 156-176 of mouse telomerase RNA (SEQ ID NO: 270), at positions 140-170 of rat telomerase RNA (SEQ ID NO: 271), at positions 339-368 of xenopus telomerase RNA (SEQ ID NO: 279), along with other conserved regions.
It is further contemplated that any nucleotide within the target telomerase RNA may be modified using the methods of the present invention, using the structural information that is available in the art. Methods of creating libraries of snoRNA genes for modification at various positions within a target RNA are known in the art (Liu, B., J. Ni, and M. J. Fournier, “Probing RNA in vivo with methylation guide small nucleolar RNAs,” Methods, 2001. 23 (3): p. 276-86).
Engineered snoRNAs
The engineered snoRNAs of the invention may be made using methods known in the art, see, e.g., (Liu, B., et al., Methods 23(3):276-86 (2001); Huang, C, et al., Methods Mol. Biol. 718:227-44 (2011)). In general, standard molecular biology techniques may be used to clone the native snoRNA gene, remove the guide sequence portion of the gene and replace the guide sequence with a guide sequence that targets 2′-O-methylation of a specific nucleotide on the target RNA. The cloned nucleic acids encoding engineered C/D box snoRNA may then be subcloned into vectors for replication of the cloned nucleic acid sequence and/or expression in vivo.
Expression of engineered snoRNAs in vivo may be effected by use of standard techniques known in the art. An engineered snoRNA can be produced in vivo in a mammal, e.g., a human patient, using gene therapy approaches known in the art. These approaches involve administration of a suitable engineered snoRNA encoding nucleic acid operably linked to suitable expression control sequences. Preferably, these sequences are incorporated into a viral vector. Suitable viral vectors for such in vivo expression include, e.g., adenoviral vectors, lentiviral vectors, baculoviral vectors, Epstein Barr viral vectors, papovaviral vectors, vaccinia viral vectors, herpes simplex viral vectors, and adeno associated virus (AAV) vectors. The viral vector can be a replication-defective viral vector. A preferred adenoviral vector has a deletion in its E1 gene or E3 gene. When an adenoviral vector is used, preferably, the mammal is not exposed to a nucleic acid encoding a selectable marker gene.
Expression of engineered snoRNAs in cell lines in vivo may also be performed using transformation, or injection methods known in the art for the cell line being used. See, for example, Huang, C, et al., Methods Mol. Biol. 718:227-44 (2011); 718:227-44 and Ge, J., et al., Rna 16:1078-1085 (2010). The nucleic acid sequences encoding the engineered snoRNAs may be cloned into vectors for expression in cells in the same manner as nucleic acid sequences encoding for proteins.
In certain embodiments, engineered snoRNAs are provided that direct 2′-O-methylation of nucleotides in or near the pseudoknot region of human telomerase RNA (SEQ ID NO: 266), positions 171-186 as highlighted:









1
GGGUUGCGGA GGGUGGGCCU GGGAGGGGUG GUGGCCAUUU UUUGUCUAAC CCUAACUGAG



 


61
AAGGGCGUAG GCGCCGUGCU UUUGCUCCCC GCGCGCUGUU UUUCUCGCUG ACUUUCAGCG


 


121
GGCGGAAAAG CCUCGGCCUG CCGCCUUCCA CCGUUCAUUC UAGAGCAAAC AAAAAAUGUC


 


181
AGCUGCUGGC CCGUUCGCCC CUCCCGGGGA CCUGCGGCGG GUCGCCUGCC CAGCCCCCGA


 


241
ACCCCGCCUG GAGGCCGCGG UCGGCCCGGG GCUUCUCCGG AGGCACCCAC UGCCACCGCG


 


301
AAGAGUUGGG CUCUGUCAGC CGCGGGUCUC UCGGGGGCGA GGGCGAGGUU CAGGCCUUUC


 


361
AGGCCGCAGG AAGAGGAACG GAGCGAGUCC CCGCGCGCGG CGCGAUUCCC UGAGCUGUGG


 


421
GACGUGCACC CAGGACUCGG CUCACACAUG C






Examples of nucleic acids encoding guide sequences upstream from the D box in a C/D box snoRNA (represented as the highlighted DNA sequence encoding the snoRNA) are shown below, with N representing any nucleotide. The guide sequences are engineered to modify the base complementary to the base shown in bold by their location upstream from Box D of the snoRNA. Guide sequences with and without the Box D sequence are shown for modification of each position below.
Guide Sequences and Box D Sequences:









(SEQ ID NO: 285)



Position 171-ACATTTTTTGTTNCTGA



 



(SEQ ID NO: 286)



Position 172-GACATTTTTTGTNCTGA



 



(SEQ ID NO: 287)



Position 173-TGACATTTTTTGNCTGA



 



(SEQ ID NO: 288)



Position 174-CTGACATTTTTTNCTGA



 



(SEQ ID NO: 289)



Position 175-GCTGACATTTTTNCTGA



 



(SEQ ID NO: 290)



Position 176-AGCTGACATTTTNCTGA



 



(SEQ ID NO: 291)



Position 177-CAGCTGACATTTNCTGA



 



(SEQ ID NO: 292)



Position 178-GCAGCTGACATTNCTGA



 



(SEQ ID NO: 293)



Position 179-TGCAGCTGACATNCTGA



 



(SEQ ID NO: 294)



Position 180-CTGCAGCTGACANCTGA



 



(SEQ ID NO: 295)



Position 181-CCTGCAGCTGACNCTGA



 



(SEQ ID NO: 296)



Position 182-GCCTGCAGCTGANCTGA



 



(SEQ ID NO: 297)



Position 183-GGCCTGCAGCTGNCTGA



 



(SEQ ID NO: 298)



Position 184-GGGCCTGCAGCTNCTGA



 



(SEQ ID NO: 299)



Position 185-CGGGCCTGCAGCNCTGA






Guide Sequences Only:









(SEQ ID NO: 300)



Position 171-ACATTTTTTGTT



 



(SEQ ID NO: 301)



Position 172-GACATTTTTTGT



 



(SEQ ID NO: 302)



Position 173-TGACATTTTTTG



 



(SEQ ID NO: 303)



Position 174-CTGACATTTTTT



 



(SEQ ID NO: 304)



Position 175-GCTGACATTTTT



 



(SEQ ID NO: 305)



Position 176-AGCTGACATTTT



 



(SEQ ID NO: 306)



Position 177-CAGCTGACATTT



 



(SEQ ID NO: 307)



Position 178-GCAGCTGACATT



 



(SEQ ID NO: 308)



Position 179-TGCAGCTGACAT



 



(SEQ ID NO: 309)



Position 180-CTGCAGCTGACA



 



(SEQ ID NO: 310)



Position 181-CCTGCAGCTGAC



 



(SEQ ID NO: 311)



Position 182-GCCTGCAGCTGA



 



(SEQ ID NO: 312)



Position 183-GGCCTGCAGCTG



 



(SEQ ID NO: 313)



Position 184-GGGCCTGCAGCT



 



(SEQ ID NO: 314)



Position 185-CGGGCCTGCAGC






The guide sequences provided above may be used to modify any of the C/D snoRNA sequences to form an engineered snoRNA. The C/D box snoRNA only needs to be modified to position the guide sequence relative to the D box sequence as shown.
As an example of how C/D box snoRNAs may be modified according to the invention, the following nucleic acids encoding engineered snoRNA molecules are shown for illustrative purposes. The D box sequence and guide sequence are underlined. The base complementary to the nucleotide to be modified is shown in bold type.
SNORD73a native sequence (with an AUGA D′ box sequence):







(SEQ ID NO: 74)


AATAAGTGATGAAAAAAGTTTCGGTCCCAGATGATGGCCAGTGATAAC


 


AACATTTTTCTGATGTT.






SNORD73a sequence engineered for modification of human telomerase at position 176:







(SEQ ID NO: 315)


AATAAGTGATGAAAAAAAGCTGACATTTTGATGATGGCCAGTGATAAC


 


AACATTTTTCTGATGTT.






SNORD73a sequence engineered for modification of human telomerase at position 181:







(SEQ ID NO: 316)


AATAAGTGATGAAAAAACCTGCAGCTGACGATGATGGCCAGTGATAA


 


CAACATTTTTCTGATGTT.






SNORD111A native sequence (with a CUGA D′ box sequence):







(SEQ ID NO: 120)


CAGCCTGAAATGATGACTCTTTAAAAAATTTCATGTCTCTTCTCTGACA


 


TTTTTCTCTGGACACAGTTTTTGCCTTATGAATCTGATCAGGCTG.






SNORD111A sequence engineered for modification of human telomerase at position 176:







(SEQ ID NO: 317)


CAGCCTGAAATGATGACTCTTTAAAAAATTAGCTGACATTTTTCTGAC


 


ATTTTTCTCTGGACACAGTTTTTGCCTTATGAATCTGATCAGGCTG.






SNORD111A sequence engineered for modification of human telomerase at position 181:







(SEQ ID NO: 318)


CAGCCTGAAATGATGACTCTTTAAAAAATTCCTGCAGCTGACTCTGAC


 


ATTTTTCTCTGGACACAGTTTTTGCCTTATGAATCTGATCAGGCTG.






SNORD113-1 native sequence (with a CUGA D′ box sequence):







(SEQ ID NO: 123)


AAAGTGAGTGATGAATAGTTCTGTGGCATATGAATCATTAATTTTGATT


 


AAACCCTAAACTCTGAAGTCC.






SNORD113-1 sequence engineered for modification of human telomerase at position 176:







(SEQ ID NO: 319)


AAAGTGAGTGATGAATAGTTCTGTGGCATATGAATCATTAATTTTGAT


 


AGCTGACATTTTTCTGAAGTCC.






SNORD113-1 sequence engineered for modification of human telomerase at position 181:







(SEQ ID NO: 320)


AAAGTGAGTGATGAATAGTTCTGTGGCATATGAATCATTAATTTTGAT


 


CCTGCAGCTGACTCTGAAGTCC.






Examples of C/D box snoRNAs include those modified from the yeast snR52 wild type sequence to target specific nucleotides within a pseudoknot of the telomerase RNA, shown below. The base complementary to the nucleotide to be modified is shown in bold type.
Native snR52 sequence (with CTGA D Box sequence):







(SEQ ID NO: 236)


TACTATGATGAATGACATTAGCGTGAAC ATCTCTGATACAAAATCGAA


 


AGATTTTAGGATTAGAAAAACTTATGTTGCCTTCCTTCTGAAA.






Guide sequence targeting position 804 of yeast telomerase (TLC1):









(SEQ ID NO: 321)



AATAGATTT  TTTNCTGA.






Guide sequence targeting position 805 of yeast telomerase (TLC1):









(SEQ ID NO: 322)



GAATAGATT  TTTNCTGA.






Guide sequence targeting position 806 of yeast telomerase (TLC1):









(SEQ ID NO: 323)



TGAATAGA  TTTNCTGA.






Guide sequence targeting position 809 of yeast telomerase (TLC1):









(SEQ ID NO: 324)



CAGTGAAT  GATNCTGA.






Guide sequence targeting position 810 of yeast telomerase (TLC1):









(SEQ ID NO: 325)



TCAGTGAA  AGANCTGA.






Guide sequence targeting position 811 of yeast telomerase (TLC1):









(SEQ ID NO: 326)



TTCAGTGA  TAGNCTGA.






As should be apparent from the above illustrative examples, a guide sequence of an engineered snoRNA is designed to base pair with the target telomerase so that the nucleotide to be modified is complementary to the base 5 bases upstream from the D or D′ box of the snoRNA. The guide sequences of the present invention can be used in any engineered snoRNA according to this rule.
It is contemplated that the guide RNA sequences may be longer or shorter than the and 12 nucleotide guide sequences illustrated above. The guide sequences may be 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30 or greater nucleotides in length. A person of skill in the art will understand that it is possible to lengthen the guide sequence by adding complementary nucleotides to the 5′ end of the guide sequence based on the complementary sequence of the target RNA so that the base to be modified remains base paired with the Box D+5 position. A person of skill in the art will also understand that it is possible to shorten the guide sequence by removing complementary nucleotides from the 5′ end of the guide sequence so that the base to be modified remains base paired with the Box D+5 position. It is further contemplated that the guide sequences may have 1, 2, 3, 4, 5, 6, 7, 8 or more mismatched base pairing with the target RNA, depending on the length of the guide sequence.
After an engineered C/D box snoRNA is expressed in a cell, telomerase complexes containing modified telomerase RNA may be recovered from the cell using methods known in the art or using methods as described in the examples below (Qiao, F., et al., Nat. Struct. Mol. Biol. 15:634-40 (2008)). It is further contemplated that C/D snoRNA modification of the target telomerase RNA may be effected in vitro by reconstitution of the necessary components of the snoRNA modification machinery, including any snoRNA associated proteins.
Isolated telomerase complexes may be assayed in vitro as is known in the art to determine the effects of modifications. Examples of telomerase assays may be found in Zappulla, D. C., et al., (Proc. Natl. Acad. Sci. USA 101:10024-9 (2004)) and Chen, J. L. and Greider C. W. (Proc. Natl. Acad. Sci. USA 102:8080-8085 (2005)). In vitro assays comparing modified telomerase with wild type telomerase activity may be used to determine whether the 2′-O-methylation effected by the engineered snoRNA causes an increase or decrease in telomerase activity.
The in vivo activity of modified telomerase with a modified telomerase RNA may be measured by determining the average length of telomeres in cells containing the engineered snoRNA as compared to the average length of telomeres in cells with unmodified telomerase RNA. Methods for determining telomere length are known in the art, including, e.g., PCR methods, southern blot methods and fluorescent in situ hybridization methods (Allshire R. C. et al., (1989) Nucleic Acids Res. 17:4611-4627 (1989); Rufer, N. et al., Nat. Biotechnol. 16: 743-747 (1998); Cawthon, R. M., Nucleic Acids Res. 30 (10):e47)(2002)). The presence of longer telomeres in cells having modified telomerase RNA suggests an increase in telomerase activity from the modification while the presence of shorter telomeres in cells having modified telomerase RNA suggests an decrease in telomerase activity from the modification.
Modified telomere RNA may be isolated from cells using methods known in the art. Primer extension methods known in the art may be used to determine whether or not the targeted position of the telomere RNA was 2′-O-methylated (Ge, J., et al., Rna 16:1078-1085 (2010)).
Having now generally described the invention, the same will be more readily understood through reference to the following examples which are provided by way of illustration, and are not intended to be limiting of the present invention, unless specified.
EXAMPLES
Results
Artificial Box C/D RNA Targeting TLC1 is Efficiently Expressed
Qiao, et al, have recently shown that 2′-OH groups of the triple-helix (A804, A805 and A806) nucleotides and their adjacent nucleotides (U809, A810 and U811) within the conserved pseudoknot structure of TLC1 contribute to telomerase function in vitro ((Qiao, F., et al., Nat. Struct. Mol. Biol. 15:634-40 (2008)), (FIG. 1A), thus offering an opportunity for an in vivo functional analysis of these 2′-OH groups using RNA-guided RNA 2′-O-methylation. Six artificial box C/D guide RNAs were designed (gRNA-A804, gRNA-A805, gRNA-A806, gRNA-U809, gRNA-A810, gRNA-U811), each of which targeted one of the six nucleotides in the triple-helix region (FIG. 1A). These artificial guide RNAs were constructed based on snR52, a naturally occurring S. cerevisiae box C/D snoRNA that contains two guide sequences, one between box C and box D′ and the other between box C′ and box D (FIG. 1B). The short guide sequence between box C and box D′ or between box C′ and box D was altered to target the TLC1 nucleotides; all other nucleotide sequences of snR52 were left unchanged. The artificial box C/D RNA genes were separately inserted into a 2μ vector, with the expression of the box C/D guide RNAs under the control of the GPD promoter.
Upon transformation, the expression of guide RNA was measured using northern analysis. Northern results showed that every guide RNA was efficiently expressed (FIG. 2A, lanes 3-8).
Artificial Box C/D Guide RNA is Functionally Active In Vivo
To ensure that the artificial box C/D guide RNA had a sufficient level of activity, a primer extension-based 2′-O-methylation assay to detect 2′-O-methylation of TLC1 at the target sites was carried out. It is well established that at low dNTP concentrations, primer extension will stop/pause precisely one nucleotide before the 2′-O-methylated site (Maden, B. E., et al., Biochimie 77:22-9 (1995)). When a guide RNA was expressed, a stop/pause signal corresponding to its target site was clearly detected under low-dNTP conditions (FIG. 2B, lanes 4, 6, 8, 10, 12 and 14). As expected, when high dNTP concentrations were used, the stop/pause signal was barely detected (FIG. 2B, lanes 3, 5, 7, 9, 11 and 13). Thus, these results demonstrated that each guide RNA was capable of guiding TLC1 2′-O-methylation at its target site.
Given that 2′-O-methylation efficiency is important for determining the degree to which the modification influences telomerase activity, the level of 2′-O-methylation at each target site was further quantified. A recently developed ligation based assay was used, in which a pair of DNA primers are aligned with the RNA substrate upon hybridization, leaving the ligation junction (nick) 5′ or 3′ of the test nucleotide in the RNA substrate (Saikia, M., et al., Rna 12:2025-33 (2006)) (FIG. 2C). If the test nucleotide is 2′-O-methylated, the two primers will not be ligated if the ligation junction is placed 3′ of the modified nucleotide (discriminating or D primer pair), but they will be quantitatively ligated if the junction is placed 5′ of the modified nucleotide (non-discriminating or ND primer pair). If the test nucleotide is not 2′-O-methylated, the two primers (either D or ND primer pair) will be quantitatively ligated regardless of where the junction is (FIG. 2C). The ligation efficiency should correlate well with the modification level at the test site. Comparison of the ligation ratios will thus allow quantification of 2′-O-methylation at the test nucleotide.
FIGS. 2D and 2E show the ligation experiments using TLC1 RNA harvested after 30 and 590 generations, respectively. When the ND primer pair was used, ligation efficiency (the ratio of the ligated product to the loading control) was about the same for all TLC1 RNAs at all sites tested, including untargeted TLC1 RNA (con.) and gRNA targeted TLC1 RNA (FIGS. 2D and 2E, compare even-numbered lanes). However, when the D primer pair was used, a drastic reduction in ligation was observed in reactions where TLC1 RNA was isolated from cells expressing gRNAs (FIGS. 2D and 2E, compare lades 3, 7, 11, 15, 19 and 23 with other odd-numbered lanes). These results indicated a high level (70-90%) of 2′-O-methylation at all target sites regardless of the number of cell generations (30 or 590 generations) (compare FIG. 2D with FIG. 2E, and compare targeted lanes with untargeted control lanes). These results also indicated that 2′-Omethylation was target specific, as reduced ligation was detected only in reactions where a target-specific gRNA was expressed and a D primer pair for the respective target site was used (FIG. 2D, FIG. 2E, and data not shown).
2′-O-Methylation in the Triple-Helix Region does not Change TLC1 RNA Levels
Whether 2′-O-methylation in the triple-helix region would affect TLC1 RNA levels was then tested. Using northern analysis, the levels of TLC1 RNA in wild-type control cells and in cells expressing various artificial gRNAs were assessed. Total RNAs were isolated from these cells after different numbers of generations, and northern analysis was carried out using a TLC1-specific probe and a U1-specific probe as an internal control. The signals of TLC1 RNA relative to U1 RNA were virtually identical in all the cells after 30, 310 and 590 generations (FIG. 3A), indicating that targeted 2′-Omethylation had no effect on steady-state levels of TLC1 RNA.
2′-O-Methylated TLC1 RNA is Assembled into Telomerase RNP
To determine whether 2′-O-methylated TLC1 RNA was incorporated into telomerase RNP, a glycerol gradient analysis was carried out. TLC1 RNA from either the control strain or the strain expressing gRNA-U809 peaked in the same fractions, just as U1 snRNP did in both strains (FIG. 3B). The RNA from the telomerase RNP peaks was then isolated and the 2′-O-methylation assay was performed. Although no 2′-O-methylation signal was observed in control TLC1, RNA (FIG. 3C; lanes 1 and 2), a clear 2′-Omethylation signal corresponding to U809 was detected in TLC1 RNA isolated from cells expressing gRNA-U809 (lanes 3 and 4). Thus, 2′-O-methylated TLC1 RNA appeared to be incorporated into the telomerase RNP.
To further confirm these gradient results, an independent approach was performed, namely Est2p-co-precipitation assay. A strain in which the telomerase reverse transcriptase gene EST2 is fused with a protein A tag (Friedman, K. L., et al., Genes Dev. 13:2863-74 (1999)) was used in this approach.
Upon transformation with the plasmid containing an artificial box C/D RNA gene, cells were harvested, and Est2p was pulled down through protein A-IgG precipitation. Western blotting was used to measure the precipitated Est2p. As shown in FIG. 3D, a nearly identical amount of Est2p was precipitated [compare the intensity of the Est2 band in lanes 1-8 (Est2-tagged lanes)]. As a control, when untagged strain was used, an Est2p was detected (lane 9). RNA co-precipitated with Est2p was also recovered and analyzed. Northern blotting indicated that TLC1 RNA was efficiently co-precipitated with Est2p regardless of whether cells were transformed with a plasmid containing no gRNA gene (lane 8), a random box C/D RNA gene (lane 1; control) or any one of the six artificial box C/D RNA genes (lanes 2-7). 2′-O-methylation was further assayed, and these experiments showed that Est2p-associated TLC1 RNA, isolated from cells expressing a gRNA, was efficiently 2′-O-methylated at the expected target site (FIG. 3E). Thus, it appears that 2′-O-methylated TLC1 RNA is efficiently incorporated into telomerase RNP (at least associated with Est2p).
In Vitro Functional Assay Indicates that 2′-O-Methylation at U809 (Adjacent to the Triple-Helix) Reduces Telomerase Activity
To assess whether 2′-O-methylation at the nucleotides in and near the triple-helix structure affects function, the in vitro telomerase activity assay was carried out (Friedman, K. L., et al., Genes Dev. 13:2863-74 (1999)) using the Est2p-bound fractions described above. As shown in FIG. 4, targeted 2′-Omethylation at position U809 resulted in a substantial reduction of telomerase activity (FIG. 4A, lanes 9 and 10; FIG. 4B). When A804 or A805 was targeted by the artificial gRNAs, a relatively small but statistically significant enhancement of telomerase activity was observed (FIG. 4A, compare lanes 3-6 with lanes 1 and 2; FIG. 4B). 2′-O-methylation at the other sites had no significant effect on telomerase activity (FIGS. 4A and 4B).
A804 and A805 are in the triple-helix structure, and U809 is in a nearby stem adjacent to the triple-helix (FIG. 1A). The fact that 2′-O-methylation at U809 reduced telomerase activity is consistent with the previous in vitro study by Qiao, et al., who showed that combined substitution of the 2′-OH groups of all three adjacent nucleotides (U809, A810 and U811) with 2′-H groups resulted in diminished telomerase activity. In contrast, targeted 2′-O-methylation directed at the triple-helix nucleotide A804 or A805 resulted in no reduction of telomerase activity; rather, a slight increase in telomerase activity was observed. This observation is different from that made by Qiao, et al., who show a substantial reduction of telomerase activity when the 2′-OH groups of all three triple-helix nucleotides are simultaneously changed to 2′-H groups.
This apparent inconsistency may be due to the fact that the 2′-OH groups were changed to 2′-O-methyl groups whereas in the previous study, the 2′-OH groups were changed them to 2′-H groups.
A804, A805 and U809 in the Triple-Helix Region are Key 2′-O-methylation Targets for Influencing Telomerase Activity In Vivo
The effect of the six artificial guide RNAs on chromosome end maintenance in vivo was then assessed. Using Southern blotting, telomere length in cells expressing these artificial gRNAs was monitored. As shown in FIG. 5, when gRNA-U809 was expressed, chromosome ends progressively shortened with time [compare lanes 29 and 30 (590 generations) with lanes 27 and 28 (310 generations) and with lanes 25 and 26 (30 generations) or lanes 31 and 32 (30 generations)]. Interestingly, the chromosome ends moderately lengthened when gRNA-A804 or gRNA-A805 was expressed (compare lanes 11 and 12 with lanes 9 and 10, and lanes 7 and 8; also compare lanes 17 and 18 with lanes 15 and 16, and lanes 13 and 14). In contrast, no apparent changes in telomere length were detected in cells expressing any other gRNAs (lanes 19-24 and 33-44) or no gRNA (data not shown). These results are consistent with the in vitro assay results described above (also see Discussion below), pinpointing three critical nucleotides: A804 and A805 for lengthening and U809 for shortening. The other sites appeared to be less important for telomerase activity when targeted individually.
Targeted 2′-O-Methylation Influences Telomerase Activity as Shown by the Telomere Position Effect Assay
To further prove the effectiveness of the in vivo approach, an independent phenotypic assay involving the yeast strain (yHK53 rad52Δ::KanMX)(37) was used in which URA3 is inserted into chromosome VII near its end. Under normal conditions, the chromosome ends are stable and URA3 is silenced by the telomere position effect (Gottschling, D. E., et al., Cell 63:751-62 (1990)), thus allowing cells to grow on 5-FOA medium. When the chromosome ends are progressively shortened, URA3 is, however, progressively activated, which results in cell death on 5-FOA containing medium. Using this assay, a clear progressive growth defect for cells expressing gRNA-U809 was observed. In contrast, no growth defect on 5-FOA medium was observed when cells were transformed with any other gRNAs targeting a single nucleotide in the triple-helix region or with a control box C/D guide RNA containing a random guide sequence (FIG. 6A).
To confirm this observation, the telomere length of chromosome VII was measured using Southern analysis. Whereas no change in telomere length was detected when cells expressed a random (control) gRNA (FIG. 6B; compare lane 1 with lane 2), substantial telomere shortening was observed when cells were transformed with gRNAU809 (compare lane 3 with lane 4). Interestingly, a moderate lengthening of the end of chromosome VII was observed when cells received gRNA-A804 (compare lane 5 with lane 6), which is consistent with what was observed in other experiments (see FIGS. 4 and 5). Taken together, these results indicate that targeted telomerase RNA 2′-O-methylation is a very effective strategy for blocking telomerase activity in vivo.
Discussion
Using RNA-guided RNA modification, 2′-O-methylation sites were introduced into specific nucleotides in or adjacent to the triple-helix structure of S. cerevisiae TLC1 RNA, thereby affecting telomerase activity in vivo. Specifically, 2′-O-methylation at U809 resulted in telomere shortening, whereas 2′-O-methylation at A804 and A805 led to moderate lengthening of telomeres. These results appear to be consistent with the notion that the 2′-OH groups of the nucleotides within the triple-helix and the nearby stem contribute to function (directly or indirectly) (Qiao, F., et al., Nat. Struct. Mol. Biol. 15:634-40 (2008)). These results also suggest that RNA-guided RNA modification can serve as an effective tool for regulating telomerase activity (and RNA function in general) in vivo. With respect to telomerase function, Qiao, et al. demonstrated, using an in vitro system, that the 2′-OH groups of nucleotides in the triple-helix region, which are proximal to the catalytic active site, contribute to telomerase activity in vitro (Qiao, F., et al., Nat. Struct. Mol. Biol. 15:634-40 (2008)). Specifically, they show that the simultaneous changing of the 2′-OH groups of the triple-helix nucleotides (A804, A805, and A806) to 2′-H groups results in a substantial reduction in telomerase activity.
When the nucleotides (U809, A810 and U811) adjacent to the triple-helix structure are simultaneously changed to 2′-deoxy nucleotides, a substantial reduction of in vitro telomerase activity was observed. The above results show a clear reduction of telomerase activity both in vitro (FIG. 4) and in vivo (FIGS. 5 and 6) when U809, one of the three nucleotides adjacent to the triple-helix structure, was targeted for 2′-O-methylation, although targeting of either A810 or U811 did not lead to the reduction of telomerase activity. The above results thus suggest that it is the 2′-OH group of U809, rather than the 2′-OH groups of A810 and U811, that contributes to function. This approach added a methyl group to the sugar ring, thus the possibility cannot be excluded that such a modification disrupted the local structure of the RNA, thereby resulting in the reduction of telomerase activity.
Rather surprisingly, telomere lengthening was detected when 2′-O-methylation was introduced into either A804 or A805, two of the three triple-helix nucleotides (FIG. 5). This enhancing effect is in contrast to the inhibitory effect previously observed when the 2′-OH groups of the triple-helix nucleotides were changed to 2′-H groups (Qiao, F., et al., Nat. Struct. Mol. Biol. 15:634-40 (2008)). It is conceivable that if the 2′-OH group of A804 and/or A805 contributes directly to catalysis (as U809 does), changing the 2′-OH group to either 2′-H or 2′-OMethyl should dramatically alter its chemical properties (e.g., preventing hydrogen bond donation), thus resulting in a reduction (rather than an enhancement) of telomerase activity. Without wishing to be bound by theory, one possible explanation is that the 2′-OH groups of the triple-helix nucleotides may indirectly contribute to function (or catalysis): modifications at the 2′ position may influence the configuration of the sugar pucker, either C3′-endo or C2′-endo configuration, which may in turn affect its function. A sugar pucker with a 2′-OH favors the C3′-endo conformation when compared with a sugar pucker with a 2′-H. However, when the 2′-OH of the sugar pucker is methylated (2′-OMethyl), the C3′-endo conformation becomes even more favorable (Hou, Y. M., et al., Nucleic Acids Res. 29:976-85 (2001); Uesugi, S., et al., Tetrahedron Letters 20:4073 (1979)). This order of preference (2′-OMethyl>2′-OH>2′-H) for the C3′-endo conformation would be consistent with the observed effect of different 2′ moieties on telomerase activity if the C3′-endo (rather than C2′-endo) is the more functionally favorable conformation. Specifically, relative to 2′-OH, 2′-OMethyl enhances, while 2′-H inhibits, telomerase activity.
It is possible that it is the extensive base-pairing interactions between the guide sequence of gRNA and the target sequence of TLC RNA, rather than 2′-O-methylation per se, that has influenced telomerase activity. For instance, the basepairing may have altered TLC RNA folding, localization and even telomerase RNP assembly. However, this possibility is unlikely for at least two reasons. First, clean and specific 2′-O-methylation at target sites was detected (FIG. 2B and FIG. 3E). Second, not all gRNAs, which targeted different nucleotides in the same region, exhibited an inhibitory or enhancing effect on telomerase activity. For instance, gRNA-U809 and gRNA-A810 targeted nucleotides adjacent to each other, but only gRNA-U809 exhibited an inhibitory effect on telomerase activity. Because both gRNAs maintained almost identical complementarity with TLC1 RNA, these results suggest that the observed inhibitory effect of targeting U809 was truly 2′-O-methylation-specific rather than an antisense effect that could impact TLC1 RNA folding, localization or RNP assembly.
Likewise, the same reasoning can be used to explain the enhancing effect of targeting A804 or A805 (comparing gRNA-A804 or gRNA-A805 with gRNA-A806). It should also be noted that the artificial guide RNAs used in this study may have unintended target(s), thus raising concerns about substrate specificity. To address this issue, the guide sequences (12 nt) were used to conduct a BLAST search against the yeast genome, with an attempt to identify other potential target RNAs. This search generated only few such candidates: Six (STE24, PRM4, NAM7, SMI1, PUF3 and TUS1) for gRNA-A804 and gRNA-A805, and one (STB4) for U809. None of these potential targets have known functions in telomere maintenance. Thus, it is unlikely that the observed effects are due to the non-specific effect of modifications of unintended off-targets.
With regard to the application of RNA-guided RNA modification, it is shown herein that an artificial box C/D guide RNA can efficiently target TLC1 2′-O-methylation at specific sites. The artificial guide RNA can be constructed according to a naturally occurring box C/D snoRNA (e.g., snR52). According to the sequence/site to be targeted, only the short guide sequences of the original box C/D snoRNA need to be altered, and the remaining sequences do not have to be changed. Such an approach to target an RNA at a specific site appears to be straightforward and effective and should be applicable to many different RNA types.
Although any nucleotides of an RNA can, in theory, be targeted in vivo, control of RNA localization remains a major issue that must be addressed. It is known that box C/D snoRNA (or RNP) is localized to the nucleoli and/or Cajal bodies (Kiss, T. et al., Embo J 20:3617-22 (2001)); however, some potential target RNAs (for example, mRNA) do not co-localize with snoRNA. The distinct localization of RNAs raises the question of whether all nuclear RNAs (including those that are temporarily present in the nucleus) can be targeted for modification. Although localization studies detect snoRNAs in the nucleoli and/or Cajal bodies (Balakin, et al., Cell 86:823-34 (1996), Darzacq, X., et al., Embo J 21:2746-56 (2002)), such studies do not exclude the possibility that snoRNAs may exist in the nucleoplasm as well. Perhaps the failure to detect snoRNAs in the nucleoplasm merely reflects the fact that snoRNAs are too dilute to be detected in this subnuclear compartment. In this regard, two reports have suggested that a U2-specific guide RNA (Zhao, X., et al., Rna 8:1515-25 (2002)) and a guide RNA specific for spliced-leader RNA (a special type of spliceosomal snRNA involved in trans-splicing) (Liang, X. H., et al., Rna 8:237-46 (2002)) may both reside within the nucleoplasm rather than within the nucleolus or Cajal bodies. Such conclusions are bolstered by a recent finding that suggests the presence of a number of Drosophila melanogaster snRNA-specific guide RNAs in the nucleoplasm as well as in Cajal bodies (Deryusheva, S., et al., Mol. Biol. Cell 20(24):5250-9 (2009)). In this regard, the present inventors and others have shown that mRNA as well as pre-mRNA can be targeted by artificial guide RNAs for modification in vivo (Cavaille, J., M. et al., Nature 383:732-5 (1996); Zhao, X., et al., Nat. Methods 5:95-100 (2008)); (Karijolich and Yu, unpublished data). Thus, it appears that RNA-guided RNA modification can occur in one or a few different nuclear subcompartments, including the nucleolus, Cajal bodies and/or even the nucleoplasm, and that RNA-guided RNA modification is a highly useful approach for regulating RNA function in eukaryotic cells.
Methods
Plasmids and S. cerevisiae Strains
pSEC (snoRNA expression cassette) was constructed based on the parental yEPlac181 (a 2μ LEU2 vector kindly provided by Dr. E. M. Phizicky at University of Rochester) (Culver, G. M., et al., J Biol. Chem. 272:13203-10 (1997)). The GPD promoter region (a sequence corresponding to nucleotides −655 to 0 of TDH3) was inserted between EcoRI and BamH1. A 65-nt RNT1 element sequence (5′-TTTTTATTTCTTTCTAAGTGGGTACTGGCAGGAGTCGGGGCCTAGTTTAGAGA GAAGTAGACTCA-3′) (SEQ ID NO: 327), corresponding to part of 35S pre-rRNA 3′ ETS that is recognized by endonuclease RNT1 (RNase III activity) (Fatica, A., et al., Embo J 19:6218-29 (2000)), was inserted between BamH1 and SalI; a 55-nt snR13 termination sequence (5′-AGTAATCCTTCTTACATTGTATCGTAGCGCTGCATATATAATGCGTAAAATTT TC-3′) (SEQ ID NO: 328), corresponding to nucleotides 26 to 80 downstream of snR13, was inserted between PstI and HindIII. The pSEC cassette thus constructed contains a pair of restriction sites (SalI and PstI) flanked by the RNT1 element on the 5′ side and the snR13 termination sequence on the 3′ side (Fatica, A., et al., Embo J 19:6218-29 (2000)). These two restriction sites were then used for insertion of an snR52-based artificial box C/D RNA gene (in which one of the guide sequences was altered), resulting in the production of pSEC-gRNA-A804, pSEC-gRNA-A805, pSECgRNA-A806, pSEC-gRNA-U809, pSEC-gRNA-A810, pSEC-gRNA-U811. Upon transformation into yeast cells, the mature artificial box C/D RNA (gRNA) was efficiently expressed (FIG. 2A).
Strain yCH-001 (snR52Δ::URA3, BY4741 background) was used for analyzing the expression of snR52-based artificial gRNAs. In addition, using the KanMX4 cassette (Ma, X., et al., Embo J 24:2403-13 (2005)), deleted RAD52 was deleted from another haploid strain yHK53 (Yu, Q., et al., J. Biol. Chem. 284:740-50 (2009)) (BY4741 background; MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 Tel VII-URA3; kindly provided by Dr. X. Bi at the University of Rochester), generating a new strain (yCH-002) that no longer had the Rad52-mediated alternative telomere maintenance pathway. yCH-002 was then used for both the telomere length assay (see below) and the telomere position effect assay (see below).
A yeast strain YKF103 (kindly provided by the Cech group), in which the chromosomal EST2 gene is fused with a protein A tag, was used for IgG Immunoprecipitation assay (Friedman, K. L., et al., Genes Dev. 13:2863-74 (1999)) (see below).
Northern Blot Assay
To examine gRNA expression, total RNAs isolated from cells (yCH-001) expressing no gRNA, a control gRNA, gRNA-A804, gRNA-A805, gRNA-A806, gRNA-U809, gRNAA810, or gRNA-U811 were used for Northern blot analysis (FIG. 2A). The hybridization was performed using two 5′ end—radiolabeled DNA oligos: the first one was complementary to a snR52 sequence between box C′ and box D′ (5′-GTTTTTCTAATCCTAAAATCTTTCGATTTT-3′) (SEQ ID NO: 329), and the second one was complementary to U1 snRNA (5′-AACGTCCTTCTACTATTGGAA-3′) (SEQ ID NO: 330).
To check whether 2′-O-methylation affects TLC1 levels, yeast strain yCH-002 was transformed with pSEC-gRNA-Control, pSEC-gRNA-A804, pSEC-gRNA-A805, pSECgRNA-A806, pSEC-gRNA-U809, pSEC-gRNA-A810, or pSEC-gRNA-U811. After 30, 310, or 590 generations, cells were collected, total RNAs isolated, and Northern blotting performed. In brief, upon electrophoresis on a 4% polyacrylamide/8 M urea gel, RNAs were transferred to a HYBOND-N+ membrane (Amersham Pharmacia), and hybridized at room temperature with two 5′ end-labeled DNA oligo probes; one was complementary to TLC1 RNA (5′-TTCTCTGTCACATCGTTCGATGTAC-3′) (SEQ ID NO: 331), and the other was complementary to U1 snRNA (5′-AACGTCCTTCTACTATTGGAA-3′) (SEQ ID NO: 332). After an overnight hybridization, the membrane was extensively washed, and TLC1 and U1 signals were revealed by autoradiography.
Northern analysis was also carried out to check whether 2′-O-methylated TLC1 RNA associated with Est2p (or was assembled onto RNP) (see Co-immunoprecipitation and Glycerol gradient assay below),
Primer Extension-Based 2′-O-Methylation Assay
A standard primer extension-based modification assay (with high and low dNTP concentrations) was performed essentially as described (42) to detect RNA 2′-O-methylation. Briefly,  ̃6 μg of total RNA, or  ̃200 ng of Co-immunoprecipitated TLC1 RNA (see below), was mixed with 5′-radiolabeled DNA oligonucleotide Detect-TLC-2Ome (5′-TTCTCTGTCACATCGTTCGATGTAC-3′) (SEQ ID NO 333), and the primer extension reaction was carried out in the presence of either 1 mM dNTPs (high) or 0.01 mM dNTPs (low).
The reactions were incubated at 42° C. for 30 min and resolved on an 8% polyacryamide/8 M urea gel.
Ligation-Based Quantitative 2′-O-Methylation Assay
Using biotinylated antisense TLC1 DNA oligonucleotide (5′-biotin-TCAATCCGAAATCCGACACTATCTC-3′) (SEQ ID NO: 334) and biotin-streptavidin affinity chromatography (Zhao, X., et al., Rna 8:1515-25 (2002), Zhao, X., et al., Rna 10:681-90 (2004)), TLC1 RNA was purified from 1 L yeast cells (OD600=7.0) that expressed no gRNA, a random (control) gRNA or gRNA targeting the nucleotides in and adjacent to the triple-helix region. Purified cellular TLC1 RNA served as the template in the subsequent ligation reaction.
To quantify the 2′-O-methylation at any particular site of TLC1 RNA, two parallel ligation reactions (discriminating and non-discriminating reactions) with two different site specific pairs of oligodeoxynucleotides were carried out at 37° C. for 30 min in the presence of 66 mM Tris-HCl (pH 7.6), 6.6 mM MgCl2, 10 mM dithiothreitol, 66 mM ATP, 15% DMSO, 0.125 U/μL T4 DNA ligase (Saikia, M., et al., Rna 12:2025-33 (2006)).
In the discriminating ligation reaction, a pair of discriminating DNA oligonucleotides (D oligo pair) was used to hybridize with TLC1 RNA. Consequently, the two oligos were precisely aligned, placing a nick or the ligation junction (between the two oligos) on the 3′ side of U809. In the non-discriminating ligation reaction, a pair of nondiscriminating DNA oligonucleotides (ND oligo pair) was used. Upon hybridization with TLC1 RNA, the oligos were aligned, leaving a nick or the ligation junction on the 5′ side of U809. It is well established that if the target nucleotide (U809) is 2′-O-methylated, only the non-discriminating oligo pair will be ligated; however, if U809 is not 2′-O-methylated, both pairs of oligos will be ligated (Saikia, M., et al., Rna 12:2025-33 (2006)), thus providing a quantitative measurement of 2′-O-methylation at U809.
For position 804 (A804), the D oligo pair were DF-804, 5′-GAAATTTCATCAGTAAGTTCAGTGAATAGATT-3′ (SEQ ID NO: 335), and DA-804, 5′-[32P]TTTTATTTTACCTTTTTGTAGTGGG-3′(SEQ ID NO: 336); the ND oligo pair were NF-804, 5′-GAAATTTCATCAGTAAGTTCAGTGAATAGATTT-3′(SEQ ID NO: 337), and NA-804, 5′-[32P]TTTATTTTACCTTTTTGTAGTGGG-3′(SEQ ID NO: 338). Similarly, for positions 805, 806, 809, 810 and 811, the D oligo pairs were, respectively, DF-805, 5′-GGAAATTTCATCAGTAAGTTCAGTGAATAGAT-3′(SEQ ID NO: 339), and DA-805, 5′-[32P]TTTTTATTTTACCTTTTTGTAGTGG-3′(SEQ ID NO: 340), DF-806, 5′-TGGAAATTTCATCAGTAAGTTCAGTGAATAGA-3′(SEQ ID NO: 341), and DA-806, 5′-[32P]TTTTTTATTTTACCTTTTTGTAGTG-3′(SEQ ID NO: 342), DF-809, 5′-AATTTCATCAGTAAGTTCAGTGAAT-3′(SEQ ID NO: 343), and DA-809, 5′-[32P]AGATTTTTTATTTTACCTTTTTGTA-3′(SEQ ID NO: 344), DF-810, 5′-AAATTTCATCAGTAAGTTCAGTGAA-3′(SEQ ID NO: 345), and DA-810, 5′-[32P]TAGATTTTTTATTTTACCTTTTTGT-3′(SEQ ID NO: 346), and DF-811, 5′-GAAATTTCATCAGTAAGTTCAGTGA-3′(SEQ ID NO: 347), and DA-811, 5′-[32P]ATAGATTTTTTATTTTACCTTTTTG-3′(SEQ ID NO: 348); the ND oligo pairs were, respectively, NF-805, 5′-GGAAATTTCATCAGTAAGTTCAGTGAATAGATT-3′(SEQ ID NO: 349), and NA-805, 5′-[32P]TTTTATTTTACCTTTTTGTAGTGG-3′(SEQ ID NO: 350), NF-806, 5′-TGGAAATTTCATCAGTAAGTTCAGTGAATAGAT-3′(SEQ ID NO: 351), and NA-806, 5′-[32P]TTTTTATTTTACCTTTTTGTAGTG-3′(SEQ ID NO: 352), NF-809, 5′-AATTTCATCAGTAAGTTCAGTGAATA-3′(SEQ ID NO: 353), and NA-809, 5′-[32P]GATTTTTTATTTTACCTTTTTGTA-3′(SEQ ID NO: 354), NF-810, 5′-AAATTTCATCAGTAAGTTCAGTGAAT-3′(SEQ ID NO: 355), and NA-810, 5′-[32P]AGATTTTTTATTTTACCTTTTTGT-3′(SEQ ID NO: 356), and NF-811, 5′-GAAATTTCATCAGTAAGTTCAGTGAA-3′(SEQ ID NO: 357), and NA-811, 5′-[32P]TAGATTTTTTATTTTACCTTTTTG-3′(SEQ ID NO: 358). For sites U809, A810, and U811, the ligation products were 50 nucleotides long, and for sites A804, A805, and A806, the ligation products were 57 nucleotides long.
In all ligation reactions, another pair of DNA oligonucleotides (NF-1145, 5′-TTCCAAAAATTATCTAAA-3′(SEQ ID NO: 359); NA-1145, 5′-[321]TGCATCGAAGGCATTAGGAGAAGTA-3′) (SEQ ID NO: 360), which placed the ligation junction 5′ of U1145 (a non-targeting site) of TLC1 RNA, was used as a loading control.
After the ligation reaction, the radioactively labeled oligos (ligated and unligated) were resolved on an 8% polyacrylamide/8 M urea gel and quantified using a PhosphorImager (Molecular Dynamics).
Glycerol Gradient Assay
The procedure was essentially as described (Lingner, J., et al., Science 276:561-7 (1997)). Briefly, yeast cells from 2 L overnight cultures (SD leucine drop-out medium) were harvested at OD600=1.0. Pelleted cells were suspended in 4 mL of extraction buffer (20 mM Tris-acetate (pH 7.5), 300 mM potassium glutamate, 1.1 mM MgCl2, 0.1 mM EDTA, 5% glycerol, 1 mM dithiothreitol and 0.5 mM phenylmethylsulfonyl fluoride), placed in liquid nitrogen and ground with a mortar and pestle for 30 min. The lysate was concentrated three-fold in a Vivaspin ultrafiltration spin column and then loaded on the top of a 15-40% continuous glycerol gradient prepared with the extraction buffer. Ultracentrifugation (SW41Ti rotor, 150,000×g) was performed at 4° C. for 18 h. Nineteen fractions were collected, and RNA was extracted from each fraction for northern analysis (see above).
Co-Immunoprecipitation
Extracts were prepared from yeast cells (strain YKF103) expressing a control gRNA, gRNA-A804, gRNA-A805, gRNA-A806, gRNA-U809, gRNA-A810 or gRNAU811, according to the glass-bead lysis method (Friedman, K. L., et al., Genes Dev. 13:2863-74 (1999)). Briefly, 500 mL yeast cells (OD600=1.0) were lysed, by glass-bead beating, in TMG-300 NaCl buffer containing 10 mM Tris-HCl, pH 8.0, 1 mM MgCl2, 10% glycerol, 0.1 mM DTT, and 300 mM NaCl. After clarification by brief centrifugation (15,000×g at 4° C. for 5 min, repeated 3 times), total protein concentration was adjusted to 5 mg/mL. Upon addition of Tween-20 (to a final concentration of 0.5%), 500 μL of extract was mixed with 10 μL IgG Sepharose 6 Fast flow beads (GE healthcare). After overnight nutation at 4° C., the beads were collected, washed 3 times with TMG-200 NaCl-Tween buffer (10 mM Tris-HCl, pH 8.0, 1 mM MgCl2, 10% glycerol, 0.1 mM DTT, 200 mM NaCl, and 0.5 Tween) and one time with TMG-50 NaCl buffer (10 mM Tris-HCl, pH 8.0, 1 mM MgCl2, 10% glycerol, 0.1 mM DTT, 50 mM NaCl), and then resuspended in 20 μL TMG-50 NaCl buffer with 0.5 mM DTT. The beads were split into two equal aliquots of 10 μl each. One aliquot was used for in vitro telomerase activity assay (see below), and the other for TLC1 RNA extraction and analysis.
For TLC1 RNA extraction, 10 μL beads were treated with proteinase K at 37° C. for 30 min in a 200 μL reaction (10 mM Tris-HCl pH 8.0, 0.5% SDS, 0.4 mg/ml proteinase K). RNA was then PCA extracted and ethanol precipitated. Recovered TLC1 RNA was subsequently subjected to primer extension analysis (2′-O-methylation assay) and Northern blot analysis (see above).
Western Blot Assay
Western blot was performed essentially as previously described (Seto, A. G., et al., Rna 9:1323-32 (2003)). Briefly, 10 μL of immunoprecipitated beads were mixed with 10 μL 2× Laemmli loading buffer (125 mM Tris-HCl, pH 6.8, 4% SDS, 50% glycerol, 5% β-mercaptoethanol, 0.02% bromophenol blue). Upon incubation at 95° C. for 5 min, the supernatant was resolved on a 4-15% Tris-glycine gel (BioRad). Protein was then transferred to a Protran nitrocellulose membrane (Whatman) and probed with antibodies. The primary antibody was rabbit IgG (Sigma), and the secondary was goat anti-rabbit IgG-AP conjugated antibody (BioRad).
Telomerase Activity Assay
In vitro telomerase activity assay was carried out as previously described (Seto, A. G., et al., Rna 9:1323-32 (2003)). Briefly, 2 μl of Est2p-bound beads derived from immunoprecipitation (see above) were added to a final 10 μl of reaction containing 40 mM Tris-HCl, pH 8.0, 50 mM NaCl, 5% glycerol, 2.5 mM MgCl2, 0.5 mM spermidine, 0.5 mM DTT, 2.5 μM telomerase substrate (5′-TGTGGTGTGTGTGGG-3′) (SEQ ID NO: 361), 1 μL [α-32P] dGTP (10 μCi/μL), 1 μL [α-32P] dTTP (10 μCi/μL). After incubation at 30° C. for 20 min, the reaction was terminated by addition of 200 μL of proteinase K buffer (10 mM Tris-HCl pH 8.0, 0.5 SDS) and 4 μl, of proteinase K (20 mg/mL). The mixture was then incubated at 60° C. for 30 min. Nucleic acids were recovered by PCA extraction and ethanol precipitation. The primer-extended DNA products were resolved on a 14% polyacrylamide denaturing gel, and visualized by autoradiography.
Southern Analysis to Measure Telomere Length
For Southern blotting, yeast cells were grown to saturation in 20 mL SD leucine drop-out medium. The genomic DNA was subsequently extracted. Briefly, yeast cells were suspended in extraction buffer (10 mM Tris-HCl pH 8.0, 2% Triton X-100, 1% SDS, 1 mM EDTA). Upon the addition of saturated phenol and glass beads, cells were broken by vigorous vortexing. Cell extracts were treated with proteinase K ( ̃0.4 mg/mL) at 55° C. for 2 h, and genomic DNA was subsequently purified via PureLink genomic DNA spin columns (Invitrogen). The purified genomic DNA was digested with XhoI, resolved on a 0.8% agarose gel, transferred onto a HYBOND-N+ membrane (Amersham Pharmacia) and hybridized with two radiolabeled probes, one against the telomeric repeat sequence probe (5′-TGTGGGTGTGGTGTGTGGGTGTGGTG-3′) (SEQ ID NO: 362) and the other (as a control) against chromosome IV (nucleotides 31051-31075; 5′-GTCTGGCCTATGGTGCTAGTAGTAC-3′) (SEQ ID NO: 363).
For detecting URA3 integrated into chromosome VII (yCH-002 strain), purified genomic DNA was digested with PstI and hybridized with a URA3-specific probe (5′-ACATTATTATTGTTGGAAGAGGACT-3′) (SEQ ID NO: 364) and a control probe against chromosome IV (nucleotides 194700-194676; 5′-GATACACCTTCCGTTTCTGACCCAT-3′) (SEQ ID NO: 365).
Telomere Position Effect Assay
After transformation with various pSEC-gRNA plasmids, cells were plated onto solid medium, and a single colony was picked and grown to saturation in 5 mL of SD leucine drop-out medium. One microliter of the liquid culture was then withdrawn, placed in 5 mL of fresh SD leucine drop-out medium and grown to saturation again. This cycle was repeated until the cells reached 590 generations. At 310, 450 and 590 generations, an aliquot of cells was saved and stored at −80° C. for future use. To assay growth phenotype, cells from different generations were first diluted to OD600=0.1 and then plated with a series of five-fold dilutions on the SD leucine drop-out solid medium with or without 5-FOA (1 mg/mL) The growth phenotype was monitored at 30° C.

## Claims

1. A method for increasing telomere length comprising:
providing a yeast cell expressing a telomerase ribonucleoprotein comprising a yeast telomerase RNA;
providing a nucleic acid encoding, a C/D box snoRNA guide RNA that causes a 2′-O-methylation modification of nucleotide A804 or A805 in the yeast telomerase RNA to the cell in a manner that causes the guide RNA to be expressed in the cell.

2. The method of claim 1, wherein the yeast telomerase RNA is encoded by a nucleic acid comprising SEQ ID NO: 282.

3. The method of claim 1, where in the C/D box snoRNA is transcribed from a nucleic acid sequence comprising a sequence selected from SEQ ID NOs: 321 or 322.

4. The method of claim 1, wherein the process is performed in vivo.