Editing DNA methylation (section)

== Conserved function of DNA methylation ==
[[File:DNAme landscape.png|thumb|458x458px|Typical DNA methylation landscape in mammals]]
The DNA methylation landscape of vertebrates is particular compared to other organisms. In mammals, around 75% of CpG dinucleotides are methylated in [[somatic cell]]s,<ref name="pmid19842073">{{cite journal | vauthors = Tost J | title = DNA methylation: an introduction to the biology and the disease-associated changes of a promising biomarker | journal = Molecular Biotechnology | volume = 44 | issue = 1 | pages = 71–81 | date = January 2010 | pmid = 19842073 | doi = 10.1007/s12033-009-9216-2 | s2cid = 20307488 }}</ref> and DNA methylation appears as a default state that has to be specifically excluded from defined locations.<ref name="ReferenceC"/><ref>{{cite journal | vauthors = Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D | display-authors = 6 | title = DNA-binding factors shape the mouse methylome at distal regulatory regions | journal = Nature | volume = 480 | issue = 7378 | pages = 490–495 | date = December 2011 | pmid = 22170606 | doi = 10.1038/nature11086 | doi-access = free }}</ref> By contrast, the genome of most plants, invertebrates, fungi, or protists show "mosaic" methylation patterns, where only specific genomic elements are targeted, and they are characterized by the alternation of methylated and unmethylated domains.<ref name=":1">{{cite journal | vauthors = Zemach A, McDaniel IE, Silva P, Zilberman D | title = Genome-wide evolutionary analysis of eukaryotic DNA methylation | journal = Science | volume = 328 | issue = 5980 | pages = 916–919 | date = May 2010 | pmid = 20395474 | doi = 10.1126/science.1186366 | bibcode = 2010Sci...328..916Z | s2cid = 206525166 | doi-access = free | quote = Here we quantify DNA methylation in seventeen eukaryotic genomes.... | type = ScienceExpress Report }}{{open access}} Supplemental figures appear to be only accessible via the science.sciencemag.org paywall.</ref><ref>{{cite journal | vauthors = Suzuki MM, Kerr AR, De Sousa D, Bird A | title = CpG methylation is targeted to transcription units in an invertebrate genome | journal = Genome Research | volume = 17 | issue = 5 | pages = 625–631 | date = May 2007 | pmid = 17420183 | pmc = 1855171 | doi = 10.1101/gr.6163007 }}</ref>

[[File:Cytosine becomes thymine.png|thumb|Cytosine methylation then deamination to Thymine]]
High CpG methylation in mammalian genomes has an evolutionary cost because it increases the frequency of spontaneous mutations. Loss of amino-groups occurs with a high frequency for cytosines, with different consequences depending on their methylation. Methylated C residues spontaneously deaminate to form T residues over time; hence CpG dinucleotides steadily deaminate to TpG dinucleotides, which is evidenced by the under-representation of CpG dinucleotides in the human genome (they occur at only 21% of the expected frequency).<ref name="Human Genome Sequencing and Analysis">{{cite journal | vauthors = Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J | display-authors = 6 | title = Initial sequencing and analysis of the human genome | journal = Nature | volume = 409 | issue = 6822 | pages = 860–921 | date = February 2001 | pmid = 11237011 | doi = 10.1038/35057062 | doi-access = free | bibcode = 2001Natur.409..860L | hdl = 2027.42/62798 | hdl-access = free }}</ref> (On the other hand, spontaneous deamination of unmethylated C residues gives rise to U residues, a change that is quickly recognized and repaired by the cell.)

=== CpG islands ===
{{main|CpG islands}}
In mammals, the only exception for this global CpG depletion resides in a specific category of GC- and CpG-rich sequences termed CpG islands that are generally unmethylated and therefore retained the expected CpG content.<ref>{{cite journal | vauthors = Bird AP | title = CpG-rich islands and the function of DNA methylation | journal = Nature | volume = 321 | issue = 6067 | pages = 209–213 | date = 1986-05-15 | pmid = 2423876 | doi = 10.1038/321209a0 | s2cid = 4236677 | author-link = Adrian Bird | bibcode = 1986Natur.321..209B }}</ref> CpG islands are usually defined as regions with: 1) a length greater than 200bp, 2) a G+C content greater than 50%, 3) a ratio of observed to expected CpG greater than 0.6, although other definitions are sometimes used.<ref>{{cite journal | vauthors = Gardiner-Garden M, Frommer M | title = CpG islands in vertebrate genomes | journal = Journal of Molecular Biology | volume = 196 | issue = 2 | pages = 261–282 | date = July 1987 | pmid = 3656447 | doi = 10.1016/0022-2836(87)90689-9 }}</ref> Excluding repeated sequences, there are around 25,000 CpG islands in the human genome, 75% of which being less than 850bp long.<ref name="Human Genome Sequencing and Analysis" /> They are major regulatory units and around 50% of CpG islands are located in gene promoter regions, while another 25% lie in gene bodies, often serving as alternative promoters. Reciprocally, around 60-70% of human genes have a CpG island in their promoter region.<ref>{{cite journal | vauthors = Illingworth RS, Gruenewald-Schneider U, Webb S, Kerr AR, James KD, Turner DJ, Smith C, Harrison DJ, Andrews R, Bird AP | display-authors = 6 | title = Orphan CpG islands identify numerous conserved promoters in the mammalian genome | journal = PLOS Genetics | volume = 6 | issue = 9 | pages = e1001134 | date = September 2010 | pmid = 20885785 | pmc = 2944787 | doi = 10.1371/journal.pgen.1001134 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Saxonov S, Berg P, Brutlag DL | title = A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 5 | pages = 1412–1417 | date = January 2006 | pmid = 16432200 | pmc = 1345710 | doi = 10.1073/pnas.0510310103 | doi-access = free | bibcode = 2006PNAS..103.1412S }}</ref> The majority of CpG islands are constitutively unmethylated and enriched for permissive [[Histone modification|chromatin modification]] such as [[H3K4]] methylation. In somatic tissues, only 10% of CpG islands are methylated, the majority of them being located in intergenic and intragenic regions.{{cn|date=March 2024}}

=== Repression of CpG-dense promoters ===

DNA methylation was probably present at some extent in early eukaryote ancestors. In virtually every organism analyzed, methylation in promoter regions correlates negatively with gene expression.<ref name=":1" /><ref name=":2">{{cite journal | vauthors = Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, Ukomadu C, Sadler KC, Pradhan S, Pellegrini M, Jacobsen SE | display-authors = 6 | title = Conservation and divergence of methylation patterning in plants and animals | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 107 | issue = 19 | pages = 8689–8694 | date = May 2010 | pmid = 20395551 | pmc = 2889301 | doi = 10.1073/pnas.1002720107 | doi-access = free }}</ref> CpG-dense promoters of actively transcribed genes are never methylated, but, reciprocally, transcriptionally silent genes do not necessarily carry a methylated promoter. In mouse and human, around 60–70% of genes have a CpG island in their promoter region and most of these CpG islands remain unmethylated independently of the transcriptional activity of the gene, in both differentiated and undifferentiated cell types.<ref>{{cite journal | vauthors = Mohn F, Weber M, Rebhan M, Roloff TC, Richter J, Stadler MB, Bibel M, Schübeler D | display-authors = 6 | title = Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors | journal = Molecular Cell | volume = 30 | issue = 6 | pages = 755–766 | date = June 2008 | pmid = 18514006 | doi = 10.1016/j.molcel.2008.05.007 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, Schübeler D | title = Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome | journal = Nature Genetics | volume = 39 | issue = 4 | pages = 457–466 | date = April 2007 | pmid = 17334365 | doi = 10.1038/ng1990 | s2cid = 22446734 }}</ref> Of note, whereas DNA methylation of CpG islands is unambiguously linked with transcriptional repression, the function of DNA methylation in CG-poor promoters remains unclear; albeit there is little evidence that it could be functionally relevant.<ref>{{cite journal | vauthors = Schübeler D | title = Function and information content of DNA methylation | journal = Nature | volume = 517 | issue = 7534 | pages = 321–326 | date = January 2015 | pmid = 25592537 | doi = 10.1038/nature14192 | s2cid = 4403755 | bibcode = 2015Natur.517..321S }}</ref>

DNA methylation may affect the transcription of genes in two ways. First, the methylation of DNA itself may physically impede the binding of [[transcription factor|transcriptional proteins]] to the gene,<ref name="pmid20875111">{{cite journal | vauthors = Choy MK, Movassagh M, Goh HG, Bennett MR, Down TA, Foo RS | title = Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated | journal = BMC Genomics | volume = 11 | issue = 1 | pages = 519 | date = September 2010 | pmid = 20875111 | pmc = 2997012 | doi = 10.1186/1471-2164-11-519 | doi-access = free }}</ref> and second, and likely more important, methylated DNA may be bound by proteins known as [[methyl-CpG-binding domain]] proteins (MBDs). [[Methyl-CpG-binding domain protein 2|MBD]] proteins then recruit additional proteins to the locus, such as [[histone deacetylase]]s and other [[chromatin remodeling]] proteins that can modify [[histone]]s, thereby forming compact, inactive chromatin, termed [[heterochromatin]]. This link between DNA methylation and chromatin structure is important. In particular, loss of [[Methyl CpG binding protein 2|methyl-CpG-binding protein 2]] (MeCP2) has been implicated in [[Rett syndrome]]; and [[Methyl-CpG-binding domain protein 2|methyl-CpG-binding domain protein 2 (MBD2)]] mediates the transcriptional silencing of hypermethylated genes in "cancer."{{cn|date=March 2024}}

=== Repression of transposable elements ===

DNA methylation is a powerful transcriptional repressor, at least in CpG dense contexts. Transcriptional repression of protein-coding genes appears essentially limited to specific classes of genes that need to be silent permanently and in almost all tissues. While DNA methylation does not have the flexibility required for the fine-tuning of gene regulation, its stability is perfect to ensure the permanent silencing of [[transposable element]]s.<ref>{{cite journal | vauthors = Dahlet T, Argüeso Lleida A, Al Adhami H, Dumas M, Bender A, Ngondo RP, Tanguy M, Vallet J, Auclair G, Bardet AF, Weber M | display-authors = 6 | title = Genome-wide analysis in the mouse embryo reveals the importance of DNA methylation for transcription integrity | journal = Nature Communications | volume = 11 | issue = 1 | pages = 3153 | date = June 2020 | pmid = 32561758 | pmc = 7305168 | doi = 10.1038/s41467-020-16919-w | bibcode = 2020NatCo..11.3153D }}</ref> Transposon control is one of the most ancient functions of DNA methylation that is shared by animals, plants and multiple protists.<ref>{{cite journal | vauthors = Huff JT, Zilberman D | title = Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes | journal = Cell | volume = 156 | issue = 6 | pages = 1286–1297 | date = March 2014 | pmid = 24630728 | pmc = 3969382 | doi = 10.1016/j.cell.2014.01.029 }}</ref> It is even suggested that DNA methylation evolved precisely for this purpose.<ref>{{cite journal | vauthors = Yoder JA, Walsh CP, Bestor TH | title = Cytosine methylation and the ecology of intragenomic parasites | journal = Trends in Genetics | volume = 13 | issue = 8 | pages = 335–340 | date = August 1997 | pmid = 9260521 | doi = 10.1016/s0168-9525(97)01181-5 | doi-access = free }}</ref>

=== Genome expansion ===
DNA methylation of transposable elements has been known to be related to genome expansion. However, the evolutionary driver for genome expansion remains unknown. There is a clear correlation between the size of the genome and CpG, suggesting that the DNA methylation of transposable elements led to a noticeable increase in the mass of DNA.<ref>{{cite journal | vauthors = Zhou W, Liang G, Molloy PL, Jones PA | title = DNA methylation enables transposable element-driven genome expansion | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 117 | issue = 32 | pages = 19359–19366 | date = August 2020 | pmid = 32719115 | pmc = 7431005 | doi = 10.1073/pnas.1921719117 | doi-access = free | bibcode = 2020PNAS..11719359Z }}</ref>

=== Methylation of the gene body of highly transcribed genes ===

A function that appears even more conserved than transposon silencing is positively correlated with gene expression. In almost all species where DNA methylation is present, DNA methylation is especially enriched in the body of highly transcribed genes.<ref name=":1" /><ref name=":2" /> The function of gene body methylation is not well understood. A body of evidence suggests that it could regulate [[RNA splicing|splicing]]<ref>{{cite journal | vauthors = Lev Maor G, Yearim A, Ast G | title = The alternative role of DNA methylation in splicing regulation | journal = Trends in Genetics | volume = 31 | issue = 5 | pages = 274–280 | date = May 2015 | pmid = 25837375 | doi = 10.1016/j.tig.2015.03.002 | s2cid = 34258335 }}</ref> and suppress the activity of intragenic transcriptional units (cryptic promoters or transposable elements).<ref>{{cite journal | vauthors = Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D'Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJ, Haussler D, Marra MA, Hirst M, Wang T, Costello JF | display-authors = 6 | title = Conserved role of intragenic DNA methylation in regulating alternative promoters | journal = Nature | volume = 466 | issue = 7303 | pages = 253–257 | date = July 2010 | pmid = 20613842 | pmc = 3998662 | doi = 10.1038/nature09165 | bibcode = 2010Natur.466..253M }}</ref> Gene-body methylation appears closely tied to H3K36 methylation. In yeast and mammals, H3K36 methylation is highly enriched in the body of highly transcribed genes. In yeast at least, [[H3K36me3]] recruits enzymes such as histone deacetylases to condense chromatin and prevent the activation of cryptic start sites.<ref>{{cite journal | vauthors = Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL | display-authors = 6 | title = Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription | journal = Cell | volume = 123 | issue = 4 | pages = 581–592 | date = November 2005 | pmid = 16286007 | doi = 10.1016/j.cell.2005.10.023 | s2cid = 9328002 | doi-access = free }}</ref> In mammals, [[DNMT3a]] and [[DNMT3b]] PWWP domain binds to H3K36me3 and the two enzymes are recruited to the body of actively transcribed genes.{{cn|date=March 2024}}