7. DNA Methylation

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7.1. DNA Methylation

 

DNA methyltransferase (DNMTs) is responsible for covalent transmission of methyl group to the C-5 of cytosine ring of DNA and results in DNA methylation, which is a heritable event (Jin B et al., 2011) (Petryk N et al., 2021). DNA methylation that DNMTs catalyzes plays a role in epigenetic silencing of transcription (Fig.1) (Jin B et al., 2011).

 

In mammals, in any setting of the genome, DNA methylation takes place in cytosines (Lister R et al., 2009) (Jin B et al., 2011). The CpG setting in somatic cells is where the majority of DNA methylation happens; however, ¼ of the total methylations in embryonic stem cells (ESCs), occurs in a non-CpG setting (Lister R et al., 2009) (Jin B et al., 2011) (Petryk N et al., 2021).

 

The family of DNMTs, including DNMT1, DNMT2, DNMT3A, DNMT3B and DNMT3L, are responsible for controlling the DNA methylation process (Jin B et al., 2011). 

 

DNMT1, largely as a maintenance methyltransferase (Jin B et al., 2011) (Petryk N et al., 2021)., is playing a role in duplicating DNA methylation prototype to the daughter strands throughout DNA replication (Probst A V et al., 2009 as cited in Jin B et al., 2011 ) (Jin B et al., 2011).

 

The cytosine-38, in the anticodon loop of aspartic acid, is methylated by DNMT2 and in turn transmits RNA as a substitute for DNA (Goll M G et al., 2006 as cited in Jin B et al., 2011) (Jin B et al., 2011). 

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Contrary to DNMT1, DNMT3A and DNMT3B achieve de novo methylation throughout development and have a penchant for selecting unmethylated CpG dinucleotides (Jin B et al., 2011) (Petryk N et al., 2021).

 

Enhancing de novo methyltransferases capacity to attach to the methyl group donor, S-adenosyl –L-methionine (SAM), and provoking their function in vivo, achieved by the help of DNMT3L, as a homolog to DNMT3A and DNMT3B (Kareta M S et al., 2006), even though DNMT3L lacks any catalytic functionality on its own (Jin B et al., 2011).

 

Lack of DNA methylation is significantly related to the occurrence of cancer, even though, there is no evidence of associating the tumor development to the mutation or shortfall in any DNMT. Instead this may result from the essential roles of methyltransferases during embryogenesis (Jin B et al., 2011). 

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DNA Methylation Reference 

1.        Goll, M. G. et al. Methylation of tRNA Asp by the DNA Methyltransferase Homolog Dnmt2. Science (80-. ). 311, 395–398 (2006).

2.        Jin, B., Li, Y. & Robertson, K. D. DNA Methylation: Superior or Subordinate in the Epigenetic Hierarchy? Genes Cancer 2, 607–617 (2011).

3.        Kareta, M. S., Botello, Z. M., Ennis, J. J., Chou, C. & Chédin, F. Reconstitution and Mechanism of the Stimulation of de Novo Methylation by Human DNMT3L. J. Biol. Chem. 281, 25893–25902 (2006).

4.        Lister, R. et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature462, 315–322 (2009).

5.        Petryk, N., Bultmann, S., Bartke, T. & Defossez, P.-A. Staying true to yourself: mechanisms of DNA methylation maintenance in mammals. Nucleic Acids Res. 49, 3020–3032 (2021).

6.        Probst, A. V., Dunleavy, E. & Almouzni, G. Epigenetic inheritance during the cell cycle. Nat. Rev. Mol. Cell Biol.10, 192–206 (2009).

 

7.2. DNA Methylation and Histone Modifications

 

The heritable machinery for controlling gene expression is mediated by the covalent alteration of DNA and histone proteins (Jin B et al., 2011).

 

In order to regulate critical cellular mechanisms such as gene transcription, DNA replication and DNA repair, there must be significant changes in histone tails such as acetylation, methylation, phosphorylation, ubiquitination and sumoylation (Cedar H and Bergman Y., 2009 as cited in Jin B et al., 2011) (Chi P et al., 2010) (Jin B et al., 2011).

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DNA methylation occurs when trimethylation of histone on H3 lysine 9 (H3K9), H3 lysine 27 (H3K27) and H4 lysine 20 (H4K20) takes place. It is important to mention that due to the physical link between constituents of these histone methylation mechanisms and one or more DNMTs, the trimethylation above and resulting DNA methylation occurs (Jin B et al., 2011).

 

SUV39H1/2 and EZH2 for H3K9 and H3K27, respectively, interrelate directly with DNMT1, DNMT3A and DNMT3B, as the essential histone lysine methyltransferase (Lehnertz B et al., 2003) (Vire E et al., 2006 as cited in Jin B et al., 2011) (Jin B et al., 2011).

 

Transcriptional silencing occurs through recruitment of polycomb repressive complex 1 (PRC1) by EZH2, which is a part of PRC2 and catalysis trimethylation of H3K27 (Fig. 3) (Jin B et al., 2011).

 

The binding of DNMTs to some of the EZH2 target promoters is enabled through communication between EZH2 to those DNMTs (Fig. 3) (Vire E et al., 2006 as cited in Jin B et al., 2011) (Jin B et al., 2011). CpG methylation is enhanced as a result of overexpression of EZH2, whereas H3K27 methylation and DNA methylation at recognized EZH2 target genes, decreases through RNA interference knockdown of EZH2 (Fig. 3) (Vire E et al., 2006 as cited in Jin B et al., 2011) (Jin B et al., 2011).

 

Furthermore, mono- and dimethylation of H3K9 and partly H3K27 is catalyzed by another histone methyltransferase (G9A) (Fig. 2) (Tachibana M et al., 2001 and 2002) (Jin B et al., 2011).

 

Repression of the transcription of the target genes occurs as the H3K9 and DNA methylation on G9A target loci are prompted by G9A /GLP heteromeric complex (Fig. 2) (Jin B et al., 2011)  

 

Also, regulation of the gene transcription in both heterochromatin and euchromatin is mediated by Heterochromatin Protein 1 (HP1) proteins (Jin B et al., 2011).

 

The enzymatic activity of SUV39H1/2, which leads to catalysis of trimethylation at lysine 9 of H3, facilitates the attachment of HP1 to heterochromatin (Cheutin T et al., 2003 as cited in Jin B et al., 2011) (Jin B et al., 2011). However, G9A arbitrates in the dimethylation of H3K9 and consequently facilitates the HP1 attachment to euchromatin (Fig. 2) (Tachibana M et al., 2002) (Jin B et al., 2011).

 

There is also evidence that in order for the H3K9 to directly affect the DNA methylation patterns, then there is a necessity for a physical link between H3K9me-HP1 and DNMTs (Lehnertz B et al., 2003) (Fuks F et al., 2003) (Jin B et al., 2011).

 

DNA methylation and gene silencing has also been associated with histone arginine methylation (Zhao Q et al., 2009) (Jin B et al., 2011).

 

A binding target for DNMT3A is catalyzed by PRMT5, which is caused as a consequence of symmetric dimethylation of histone H4 arginine 3 (H4R3me2s) (Zhao Q et al., 2009). This, in turn, promotes methylation of the neighbouring CpG at PRMT5 target genes (Jin B et al., 2011).

 

Further to the aforementioned roles of the histone in recruiting the DMNTs, then the permanence of DNMTs are also affected by histone demethylases and methyltransferases (Esteve P O et al., 2009) (Wang J et al., 2009 as cited in Jin B et al., 2011) (Jin B et al., 2011).

 

Histone Modification Reference

1.        Cedar, H. & Bergman, Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat. Rev. Genet. 10, 295–304 (2009).

2.        Cheutin, T. et al. Maintenance of Stable Heterochromatin Domains by Dynamic HP1 Binding. Science (80-. ).299, 721–725 (2003).

3.        Chi, P., Allis, C. D. & Wang, G. G. Covalent histone modifications — miswritten, misinterpreted and mis-erased in human cancers. Nat. Rev. Cancer 10, 457–469 (2010).

4.        Esteve, P.-O. et al. Regulation of DNMT1 stability through SET7-mediated lysine methylation in mammalian cells. Proc. Natl. Acad. Sci. 106, 5076–5081 (2009).

5.        Fuks, F. The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase. Nucleic Acids Res. 31, 2305–2312 (2003).

6.        Jin, B., Li, Y. & Robertson, K. D. DNA Methylation: Superior or Subordinate in the Epigenetic Hierarchy? Genes Cancer 2, 607–617 (2011).

7.        Lehnertz, B. et al. Suv39h-Mediated Histone H3 Lysine 9 Methylation Directs DNA Methylation to Major Satellite Repeats at Pericentric Heterochromatin. Curr. Biol. 13, 1192–1200 (2003).

8.        Tachibana, M., Sugimoto, K., Fukushima, T. & Shinkai, Y. SET Domain-containing Protein, G9a, Is a Novel Lysine-preferring Mammalian Histone Methyltransferase with Hyperactivity and Specific Selectivity to Lysines 9 and 27 of Histone H3. J. Biol. Chem. 276, 25309–25317 (2001).

9.        Tachibana, M. et al. G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. Genes Dev. 16, 1779–1791 (2002).

10.     Viré, E. et al. The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439, 871–874 (2006).

11.     Wang, J. et al. The lysine demethylase LSD1 (KDM1) is required for maintenance of global DNA methylation. Nat. Genet. 41, 125–129 (2009).

12.     Zhao, Q. et al. PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing. Nat. Struct. Mol. Biol. 16, 304–311 (2009).

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7.3. DNA Demethylation

 

DNA demethylation is essential in mammalian development and tumorigenesis (Jin B et al., 2011). 

 

In the primordial germ cells (PGCs) and in the early embryo, where the DNA demethylation takes place, then this is known as an important process for their resubmission into a pluripotent state. The highest level of methylation deficit occurs in introns, intergenic regions and repeats, then in exons and promoters within PGCs (Popp C et al., 2010) (Jin B et al., 2011).

 

Cytosine deaminases are known to playa role in demethylation. They perform this activity by switching 5-methyl Cytosine (5mC) to thymine. This is followed by restoring the T-G mismatch, which substitutes thymines with cytosine (Jin B et al., 2011). 

 

There is also evidence that global DNA demethylation in murine PGCs can be affected by a deficit in activated- induced cytosine deaminase (AID) (Popp C et al., 2010) (Jin B et al., 2011). Furthermore, demethylation of pluripotency related genes throughout reprogramming of a somatic genome must be achieved by AID (Bhutani N et al., 2010) (Jin B et al., 2011). This, in turn, shows that AID possesses a vital role in deletion of DNA methylation in vivo (Jin B et al., 2011). 

 

In recent discoveries, it has been shown that functional DNA demethylation may also be facilitated through oxidation of 5 methyl Cytosine (5mC) by the TET family of hydroxylases (Fig. 4) (Tahiliani M et al., 2009) (Jin B et al., 2011).

 

DNA Demethylation Reference

1.        Bhutani, N. et al. Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature463, 1042–1047 (2010).

2.        Jin, B., Li, Y. & Robertson, K. D. DNA Methylation: Superior or Subordinate in the Epigenetic Hierarchy? Genes Cancer 2, 607–617 (2011).

3.        Popp, C. et al. Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency. Nature 463, 1101–1105 (2010).

4.        Tahiliani, M. et al. Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1. Science (80-. ). 324, 930–935 (2009).

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7.4. DNA Methylation in Cancer

 

There is a solid association between Polycomb Group (PcG) complexes such as DNMTs and cancer e.g., EZH2 is highly expressed in tumors (Jin B et al., 2011).

 

Furthermore, there is a strong link between PcG and DNA methylation. It is demonstrated that in colon cancer, where genes are exposed to tumor specific hypermethylation then there is more possibility that there is a manifestation of H3K27 methylation of these genes in normal tissue compared with the genes in which H3K27 methylation is missing (Schlesinger Y et al., 2007 as cited in Jin B et al., 2011) (Jin B et al., 2011). DNA hypermethylated genes in adult cancers are linked to the addition of two essential repressive marks to bivalent genes, i.e., H3K9me2 and H3K9me3 in embryonic carcinoma cells (Jin B et al., 2011).

 

DNA Methylation in Cancer Reference

 

1.        Jin, B., Li, Y. & Robertson, K. D. DNA Methylation: Superior or Subordinate in the Epigenetic Hierarchy? Genes Cancer 2, 607–617 (2011).

2.        Schlesinger, Y. et al. Polycomb-mediated methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat. Genet. 39, 232–236 (2007).