# Patent

## Title
Method for manufacturing transgenic caenorhabditis elegans with DNA methyltransferase and use thereof

## Abstract

Provided are transgenic Caenorhabditis elegans (C. elegans) overexpressing DNA methyltransferase 3a (Dnmt3a) and a method of producing the same. According to the method, a specific mechanism and related factors for DNA methylation mediated by Dnmt3a may be found, and a critical gene for regulating the life span of C. elegans may be identified, and therefore C. elegans may be used as an animal model for screening a drug for a DNA methylation-related disease.

## Background
STATEMENT REGARDING GOVERNMENT RIGHTS
This invention was made with government support of Republic of Korea under Technology development and application od stem cell niche control in intestinal organoid using genome-wide analysis (1711042028) awarded by Korean Ministry of Science, ICT and Future Planning. The government has certain rights in the invention.


CROSS-REFERENCE TO RELATED APPLICATION
This application claims priority to and the benefit of Korean Patent Application No. 2015-0104475, filed on Jul. 23, 2015, the disclosure of which is incorporated herein by reference in its entirety.
BACKGROUND
1. Field of the Invention
The present invention relates to transgenic Caenorhabditis elegans overexpressing DNA methyltransferase 3a (Dnmt3a) and a method of producing the same.
2. Discussion of Related Art
DNA methylation is an epigenetic modification, and involved in the regulation of gene expression, the development of mammals, aging, and the biology of cancer. In mammals, DNA methyltransferases (DNMTs) serve to introduce methyl groups to the fifth carbon of cytosines (m5CpGs) present in cytosine-guanine (CpG) dinucleotide sequences. Such cytosine methylation serves as an important role in gene expression by providing a binding site for proteins and altering chromatin structure between DNA and histones. An epigenetic marker generated by the DNA methylation allows genes in different tissues to maintain various gene expression patterns depending on cell type.
Also, the DNA methylation is the critical factor for forming heterochromatin, involved in various processes such as the inactivation of X-chromosomes, genetic imprinting, gene silencing, and carcinogenesis, and, as another important function, stabilizes chromosomes by silencing a transcription factor so as to protect the integrity of genomes. Abnormal DNA methylation is associated with a variety of pathological events including cancer, and generally in cancer cells, characteristics such as DNA methylation, gene-specific DNA methylation, and hypermethylation of a specific promoter are observed. Particularly, it is reported that the expression of an abnormal Dnmt gene is associated with a variety of human cancers including liver cancer, prostate cancer, and breast cancer.
Also, the methylation of a regulatory DNA base sequence closely relates with gene transcriptional activity. An unmethylated CpG island is usually observed at an activated promoter site of a tissue-specific gene. In a region of a chromatin (euchromatin) at which gene transcription actively takes place, the DNA unmethylation and histone acetylation frequently occur at a promoter and the first exon site, and the methylation of histone H3 occurs at lysine residue, the fourth amino acid of histone H3. When the CpG is methylated, gene transcription may be directly influenced by interference with binding of a transcription factor to the methylated CpG, or the binding of the transcription factor may be indirectly interfered with another protein binding to the methylated CpG as a result.
In mammals, the DNMTs are divided into four types, in which the Dnmt3 family can originally methylate CpGs, but the Dnmt1 family serves to maintain a methylation pattern during the replication of DNA. The Dnmt3 family includes Dnmt3a, Dnmt3b, and Dnmt3L, in which Dnmt3a and Dnmt3b are original methyltransferases, and Dnmt3L is a modulator.
Meanwhile, the DNA methylation is phylogenetically variable. Unlike Arabidopsis thaliana which has been widely researched as a model plant, it is known that DNA methylation rarely occurs in most invertebrate animal models such as yeasts, drosophilae, and Caenorhabditis elegans (C. elegans). Particularly, genes of C. elegans are easily manipulated and have a small size, and therefore a great number of C. elegans can be simultaneously grown in vitro at a relatively low cost. C. elegans hatches from its egg and develops into an adult through four stages including L1, L2, L3, and L4, which takes only about three days, and thus it is suitable for an animal experiment. Since C. elegans has a simple body structure, consists of only 959 cells except a reproductive cell, and has a transparent body, it is easy to directly observe its inside by a microscope.
Also, the cell lineage of C. elegans from a fertilized egg to an adult has been completely identified, and as the result of the genome project, it is known that C. elegans has three times as many as the number of chromosomes of a yeast and about 2⁄3 of the number of chromosomes of a human. 40% of the chromosomes of C. elegans are similar to those of the human, and C. elegans shares 75% of five thousand human disease genes that have been known so far. Therefore, C. elegans is considered a good model system for human disease research.
SUMMARY OF THE INVENTION
Accordingly, the inventors completed transgenic C. elegans overexpressing Dnmt3a on the assumption that C. elegans is able to be a good animal model to find out a complicated regulation mechanism and a pathological role of DNA methylation due to ease of genetic manipulation and unmethylation of DNA.
Therefore, the present invention is directed to providing transgenic C. elegans overexpressing Dnmt3a, and a method of producing the same.
However, the technical objectives to be accomplished by the present invention are not limited to the above-described objectives, and other objectives not described herein will be fully understood by those of ordinary skill in the art from the following descriptions.
In one aspect, the present invention provides transgenic C. elegans overexpressing Dnmt3a.
In one exemplary embodiment of the present invention, the C. elegans may be used as an animal model for DNA methylation-related disease research.
In another exemplary embodiment of the present invention, the DNA methylation-related disease may be cancer.
In still another exemplary embodiment of the present invention, the Dnmt3a may consist of the amino acid sequence of SEQ ID NO: 1.
In another aspect, the present invention provides a method of producing transgenic C. elegans, which includes (a) constructing a recombinant vector containing a Dnmt3a gene; (b) injecting the recombinant vector into C. elegans; and (c) irradiating the C. elegans with UV rays.
In one exemplary embodiment of the present invention, the Dnmt3a gene may consist of the base sequence of SEQ ID NO: 2.
In another exemplary embodiment of the present invention, the recombinant vector in operation (a) may further contain a green fluorescent protein (GFP) gene.
In still another exemplary embodiment of the present invention, the recombinant vector in operation (a) may be cloned by introducing the Dnmt3a gene and the GFP gene into a vector having a promoter of a heat-shock protein.
In yet another exemplary embodiment of the present invention, the recombinant vector in operation (a) may be cloned by introducing the Dnmt3a gene and the GFP gene into a vector having a promoter of a large ribosomal subunit.
In yet another exemplary embodiment of the present invention, the recombinant vector in operation (b) may be injected into C. elegans by microinjection.



BRIEF DESCRIPTION OF THE DRAWINGS
The above and other objects, features and advantages of the present invention will become more apparent to those of ordinary skill in the art by describing in detail exemplary embodiments thereof with reference to the accompanying drawings, in which:
FIG. 1 shows an electrophoresis result obtained by constructing a Dnmt3a-GFP-L4455 vector by inserting Dnmt3a-GFP fusion DNA, and then treating the vector with restriction enzyme NcoI;
FIG. 2 shows fluorescent microscopic images obtained by injecting each of a Dnmt3a-GFP-L4043 vector (Phsp-16.2::Dnmt3a::GFP) and a Dnmt3a-GFPL4455 vector (Prpl-28::Dnmt3a::GFP) into wild-type C. elegans N2 and then treating the C. elegans N2 with heat to induce GFP expression;
FIG. 3 shows electrophoresis results for confirming a fragment size, which are obtained by treating C. elegans with restriction enzymes KpnI and NcoI in order to determine whether a Dnmt3a-GFP gene is inserted into the genome of C. elegans; 
FIG. 4 shows western blotting results to determine whether a Dnmt3a-GFP fusion protein is expressed in the transgenic C. elegans (Prpl-28::Dnmt3a::GFP) of the present invention; and
FIG. 5 shows optical densities of the transgenic C. elegans (Prpl-28::Dnmt3a::GFP) of the present invention in order to determine whether the activity of a Dnmt3a protein is actually maintained.



DETAILED DESCRIPTION OF EXEMPLARY EMBODIMENTS
Exemplary embodiments of the present invention will be described in detail below with reference to the accompanying drawings. While the present invention is shown and described in connection with exemplary embodiments thereof, it will be apparent to those skilled in the art that various modifications can be made without departing from the spirit and scope of the invention.
The present invention provides transgenic C. elegans overexpressing Dnmt3a, and a method of producing the same.
The term “transformation” used herein indicates that a gene introduced from an external environment is recombined and artificially inserted into a chromosome of an animal, thereby altering a part of the characteristics of the animal.
In the present invention, the transgenic C. elegans may be used as an animal model for studying a mechanism, regulation of a life span, and a disease, which are associated with DNA methylation, and in this case, there is no limit to a DNA methylation-related disease, which is preferably cancer.
In the present invention, a Dnmt3a protein may consist of the amino acid sequence of SEQ ID NO: 1, and a gene encoding the protein may consist of the base sequence of SEQ ID NO: 2, but the present invention is not limited thereto. That is, the Dnmt3a protein may be a polypeptide having a homology of at least about 50%, 60%, 70% or 75%, preferably at least about 80 to 90%, more preferably at least about 92 to 94%, and most preferably at least about 95%, 98%, 99% or higher with the amino acid sequence of SEQ ID NO: 1, or a polynucleotide having a homology of at least about 50%, 60%, 70% or 75%, preferably at least about 80 to 90%, more preferably at least about 92 to 94%, and most preferably at least about 95%, 98%, 99% or higher with the base sequence of SEQ ID NO: 2.
Also, the Dnmt3a protein has no limit as long as it originates from a mammal, which is preferably a human, a mouse, a rat, a dog or a pig.
Also, the present invention provides a method of producing transgenic C. elegans, the method including: (a) constructing a recombinant vector containing a Dnmt3a gene; (b) injecting the recombinant vector into the C. elegans; and (c) irradiating the C. elegans with UV rays.
In the present invention, the term “recombinant vector” is a vector used in genetic engineering, and preferably a plasmid vector, but the present invention is not limited thereto. For example, the recombinant vector may include a virus vector, a cosmid vector, a bacterial artificial chromosome (BAC), a yeast artificial chromosome (YAC) and other non-plasmid vectors.
In the present invention, the recombinant vector may further contain a marker gene which can be used to detect transformation, and at this time, there is no particular limit to the marker gene, which may be a gene of a fluorescent protein such as a green fluorescent protein (GFP) or a red fluorescent protein (RFP).
In the present invention, the recombinant vector may further contain a promoter for expressing a protein. Here, the term “promoter” refers to a DNA sequence regulating expression of a nucleic acid sequence operably linked to a specific host cell, has no particular limit as long as it is used for expression, and is preferably a promoter of a heat-shock protein or a promoter of a large ribosomal subunit. Also, the term “operably linked” indicates that one nucleic acid fragment is linked to another nucleic acid fragment, and therefore the function or expression thereof is influenced by the linked nucleic acid fragment.
Moreover, the recombinant vector of the present invention may further contain a random operator sequence, a sequence coding for a suitable mRNA ribosome-binding site and sequences regulating termination of transcription and translation.
The genes coding for the Dnmt3a protein and GFP, which are inserted into the recombinant vector, may be arranged to correspond to a transcription direction of a promoter present in the vector in order to effectively induce expression of each gene due to the activity of each promoter, and at this time, the Dnmt3a gene may be placed at an N terminus or C terminus of the GFP gene, and is preferably placed at the C terminus in order to effectively express a fusion protein.
Also, in the present invention, a method of injecting the recombinant vector into C. elegans may be any method known in the art without limitation, and is preferably microinjection with a micropipette.
Also, in the present invention, after the recombinant vector containing the Dnmt3a gene is injected into C. elegans, the Dnmt3a gene may be fused with its genome and irradiated with UV rays in order to establish a stable transformant throughout generations. Here, there is no limit to UV irradiation conditions, but about 300 larvae (L4 stage) which is in the stage right before reproductive cells become mature may be irradiated with energy of 300 J using a UV exposure instrument such as a UV crosslinker.
In one exemplary embodiment of the present invention, a polymerase chain reaction (PCR) was carried out, and the base sequence of the transgenic C. elegans was analyzed by treatment with a restriction enzyme in order to determine whether an intact Dnmt3a gene was integrated into the genome of the transgenic C. elegans. 
Also, to determine whether the Dnmt3a protein was expressed, western blotting was carried out on a nuclear extract and a cytoplasmic extract isolated from C. elegans, and since the Dnmt3a gene was fused with a GFP before being injected into C. elegans, the DNMT3a protein was capable of being indirectly identified by detecting the GFP through fluorescent microscopy.
Also, to confirm the activity of the Dnmt3a protein, analysis of a DNA methyltransferase was carried out. In the experiment, an immunoprecipitated Dnmt3a protein and a cell lysate were used, and compared to a HeLa experimental control group, all of the two samples showed the activity of the DNA methyltransferase.
Hereinafter, exemplary examples will be provided to help in understanding of the present invention. However, the following examples are merely provided to facilitate understanding of the present invention, and the scope of the present invention is not limited to the following examples.
Example 1: Culture of C. elegans 
As C. elegans, a standard wild-type Bristol strain N2 was purchased, and cultured in an E. coli BL21-seeded high growth agar plate at 20° C.
Example 2: Construction of Dnmt3a-GFP Recombinant Vector
As cloning vectors for constructing a Dnmt3a-GFP recombinant vector, a pPD122.18 (L4043) vector that has a promoter of an hsp-16.2 heat-shock protein, and a pPD129.59 (L4455) vector that has a promoter of a large ribosomal subunit rpl-28 were obtained from the C. elegans vector library provided by the Andrew Fire Group, and then cloned by the following method.
2-1. Construction of GFP-L4043 Vector
First, a pPD95.75 vector was digested with restriction enzymes BamHI and EcoRI to extract DNA from a GFP region, and the GFP DNA was inserted into the L4043 vector digested with restriction enzymes BamHI and EcoRI. Afterward, the L4043 vector containing the GFP DNA was injected to transform E. coli DH5α, and clones were obtained using an LB-ampicillin selective medium. Plasmid DNA extracted from the clone was treated with restriction enzyme PvuII and analyzed by electrophoresis, and therefore it was confirmed that the sizes of the digested DNA fragments were 2817 bp and 1658 bp as expected.
2-2. Construction of Dnmt3a-GFP-L4043 Vector
First, mouse Dnmt3a cDNA was obtained by amplifying a cDNA library by PCR with the following set of primers, running electrophoresis, and extracting the DNA fragment of 2727 bp from a gel.







Forward Primer: 


(SEQ ID NO: 3)


5′-TCATCTCACTGGATCCCCAGCAATGCCCTCCAG-3′


 


Reverse Primer:


(SEQ ID NO: 4)


5′-TCATTTTTTCTACCGGCCCCCATGTCCCTAACACACAAGC-3′






A GFP-Dnmt3a-L4043 vector was constructed by digesting the GFP-L4043 vector obtained in Example 2-1 with restriction enzymes BamHI and KpnI, and inserting the Dnmt3a cDNA into the vector. Afterward, the GFP-Dnmt3a-L4043 vector was injected to transform E. coli DH5α, and clones were obtained using an LB-ampicillin selective medium. Plasmid DNA extracted from the clone was digested with restriction enzymes NcoI and SpeI, and therefore it was confirmed that the sizes of the digested DNA fragments were 650 bp, 1120 bp, 2046 bp, and 3319 bp as expected.
2-3. Construction of Dnmt3a-GFP-L4455 Vector
To obtain only Dnmt3a-GFP fusion DNA from the Dnmt3a-GFP-L4043 vector obtained in Example 2-2, a cDNA library was amplified by PCR with the following set of primers, and the DNA fragment of 3641 bp was extracted from a gel.







Forward Primer:


(SEQ ID NO: 5)


5′-GACGCTCTCGTGGATCCCCAGCAATGCCCT-3′


 


Reverse Primer:


(SEQ ID NO: 6)


5′-GGCCGGCTAGCGAATTCTACGAATGCTATTTGTATAGTTCATCC-3′






A Dnmt3a-GFP-L4455 vector was constructed by digesting the L4455 vector with restriction enzymes BamHI and EcoRI, and inserting the Dnmt3a-GFP fusion DNA into the digested L4455 vector. Afterward, the Dnmt3a-GFP-L4455 vector was injected to transform E. coli DH5α, and clones were obtained using an LB-ampicillin selective medium. Plasmid DNA extracted from the clone was digested with restriction enzyme NcoI, and therefore it was confirmed that the sizes of the digested DNA fragments were 650 bp, 877 bp, 2046 bp, and 4602 bp as expected (refer to FIG. 1).
Example 3: Construction and Identification of Transformant
Each of the Dnmt3a-GFP-L4043 vector and Dnmt3a-GFP-L4455 vector obtained in Example 2 (50 μg/ml), and a Pmyo-3::RFP vector (100 μg/ml) containing a promoter of a myosin heavy chain (myo-3) and an RFP were injected into wild-type C. elegans N2 bp microinjection, and the first generation (F1) was screened, thereby obtaining an independent transgenic animal system.
Here, the Pmyo-3::RFP vector was used as a marker for determining whether transformation is successfully carried out. To confirm the transformation performed by DNA microinjection, C. elegans in which the Pmyo-3::RFP gene injected with Dnmt3a exhibits strong RFP fluorescence was selected, thereby screening subjects that are successfully transformed.
That is, each of the Dnmt3a-GFP-L4043 vector (Phsp-16.2::Dnmt3a::GFP) and the Dnmt3a-GFP-L4455 vector (Prpl-28::Dnmt3a::GFP) was injected into wild-type C. elegans N2, and treated with heat for 15 minutes at 37° C., and as shown in FIG. 2, green fluorescence was observed by inducing expression of GFP with response to the activity of a heat-shock promoter.
In a transgenic animal using the promoter of the large ribosomal subunit rpl-28 of C. elegans, the Dnmt3a gene may be expressed at a subject level, but when the gene of a different organism is expressed in C. elegans, since it can frequently have an adverse effect on a physiological function of a subject, a vector using the promoter of the hsp16.2 protein expressed by heat shock is also constructed, thereby producing transgenic C. elegans. 
Also, a stable transformant was induced by inserting the Dnmt3a-GFP gene into the genome of C. elegans by irradiating the transformant with UV rays. Here, about 300 larvae (L4 stage), which is in the stage right before reproductive cells become mature, were irradiated with energy of 300 J using a UV exposure instrument such as a UV crosslinker.
Finally, the insertion into the genome was confirmed by the restriction enzymes (KpnI, NcoI) fragment sizes produced after PCR amplification, and the result is shown in FIG. 3.
Example 4: Confirmation of Dnmt3a Protein Expression
Western blotting was carried out to determine whether an actual Dnmt3a-GFP fusion protein was expressed in the transgenic C. elegans (Prpl-28::Dnmt3a::GFP) produced in Example 3.
Particularly, a protein was extracted from C. elegans by a known method, and identified with an anti-Dnmt3a antibody and an anti-GFP antibody (Abiocode Inc.), and here, as a control group, a HeLa cell line transformed with the GFP gene was used.
Consequently, as shown in FIG. 4, the expression of the Dnmt3a-GFP fusion protein was observed in transgenic C. elegans (Prpl28::Dnmt3a::GFP) (indicated by the red arrow). That is, the Dnmt3a-GFP fusion protein was observed at a position corresponding to a larger size than the size of the GFP protein observed in the control group.
Example 5: Confirmation of Activity of Dnmt3a Protein
It was confirmed whether the activity of an actual Dnmt3a protein was maintained in the transgenic C. elegans (Prpl-28::Dnmt3a::GFP) produced in Example 3.
Particularly, the activity of Dnmt3a was measured using an EpiQuikTM DNA methyltransferase activity/inhibition assay kit (P-3001, Epigentek, USA). That is, DNA with a high content of cytosine was allowed to react with a cell lysate (10 μg) by which the expression of Dnmt3a was confirmed or immunoprecipitated Dnmt3a protein (12 μg), and methylated cytosine was confirmed with an anti-5-methylcytosine antibody (Epigentek). Here, a coloring solution was added to measure an optical density according to color variation, thereby allowing the comparison of the activity of Dnmt3a, and as a control group, a HeLa cell line having the activity of Dnmt3a was used.
As a result, the immunoprecipitated Dnmt3a of the present invention was expressed in the HeLa cell line, and thus had a similar activity to the immunoprecipitated Dnmt3a (control group). As shown in FIG. 5, in the activity confirming experiment using a cell lysate, the immunoprecipitated Dnmt3a of the present invention showed a higher activity than that of the HeLa cell line as the control group.
By using an animal model of the present invention, specific mechanisms and related factors for DNA methylation mediated by Dnmt3a can be understood.
Also, according to the present invention, since it is possible to define the relevance between DNA methylation and regulation of a life span, a critical gene for regulating the life span of C. elegans can be identified.
Also, according to the present invention, since it is possible to define the relevance between DNA methylation and a disease, mechanisms of the occurrence of various diseases such as cancer are found, and therefore C. elegans can be used as an animal model for drug screening in order to develop an anticancer agent.
It would be understood by those of ordinary skill in the art that the above descriptions of the present invention are exemplary, and the example embodiments disclosed herein can be easily modified into other specific forms without changing the technical spirit or essential features of the present invention. Therefore, it should be interpreted that the example embodiments described above are exemplary in all aspects, and are not limitative.

## Claims

1. Transgenic Caenorhabditis elegans (C. elegans) which overexpresses DNA methyltransferase 3 (Dnmt3), wherein the Dnmt3 consists of the amino acid sequence of SEQ ID NO: 1.

2. A method of producing transgenic Caenorhabditis elegans (C. elegans) of claim 1, the method comprising:
(a) constructing a recombinant vector containing a DNA methyltransferase 3 (Dnmt3) gene wherein the Dnmt3 gene consists of the nucleic acid sequence of SEQ ID NO: 2;
(b) injecting the recombinant vector into the C. elegans; and
(c) irradiating the C. elegans with UV rays.

3. The method of claim 2, wherein the recombinant vector in the step (a) further contains a green fluorescent protein (GFP) gene.

4. The method of claim 2, wherein the recombinant vector in the step (a) is cloned by introducing the Dnmt3 gene and a GFP gene into a vector having a promoter of a heat-shock protein.

5. The method of claim 2, wherein the recombinant vector in the step (a) is cloned by introducing the Dnmt3 gene and a GFP gene into a vector having a promoter of a large ribosomal subunit.

6. The method of claim 2, wherein the recombinant vector in the step (b) is injected into the C. elegans by microinjection.

7. A method of using a transgenic Caenorhabditis elegans (C. elegans) which overexpresses DNA methyltransferase 3 (Dnmt3), wherein the Dnmt3 consists of the amino acid sequence of SEQ ID NO: 1 in an animal model for studying a DNA methylation-related disease.

8. The method of claim 7, wherein the DNA methylation-related disease is cancer.