Editing Transcription (biology) (section)

====CpG island methylation and demethylation====

[[File:Cytosine and 5-methylcytosine.svg|thumb|300px|This shows where the methyl group is added when 5-methylcytosine is formed]]

Transcription regulation at about 60% of promoters is also controlled by methylation of cytosines within CpG dinucleotides (where 5' cytosine is followed by 3' guanine or [[CpG sites]]). [[5-methylcytosine]] (5-mC) is a [[methylation|methylated]] form of the [[DNA]] base [[cytosine]] (see Figure). 5-mC is an [[Epigenetics|epigenetic]] marker found predominantly within CpG sites. About 28 million CpG dinucleotides occur in the human genome.<ref name="pmid26932361">{{cite journal |vauthors=Lövkvist C, Dodd IB, Sneppen K, Haerter JO |title=DNA methylation in human epigenomes depends on local topology of CpG sites |journal=Nucleic Acids Res |volume=44 |issue=11 |pages=5123–32 |date=June 2016 |pmid=26932361 |pmc=4914085 |doi=10.1093/nar/gkw124 |url=}}</ref> In most tissues of mammals, on average, 70% to 80% of CpG cytosines are methylated (forming 5-methylCpG or 5-mCpG).<ref name="pmid15177689">{{cite journal |vauthors=Jabbari K, Bernardi G |title=Cytosine methylation and CpG, TpG (CpA) and TpA frequencies |journal=Gene |volume=333 |issue= |pages=143–9 |date=May 2004 |pmid=15177689 |doi=10.1016/j.gene.2004.02.043 |url=}}</ref> However, unmethylated cytosines within 5'cytosine-guanine 3' sequences often occur in groups, called [[CpG site#CpG islands|CpG islands]], at active promoters. About 60% of promoter sequences have a CpG island while only about 6% of enhancer sequences have a CpG island.<ref name="pmid32338759">{{cite journal |vauthors=Steinhaus R, Gonzalez T, Seelow D, Robinson PN |title=Pervasive and CpG-dependent promoter-like characteristics of transcribed enhancers |journal=Nucleic Acids Res |volume=48 |issue=10 |pages=5306–17 |date=June 2020 |pmid=32338759 |pmc=7261191 |doi=10.1093/nar/gkaa223 |url=}}</ref> CpG islands constitute regulatory sequences, since if CpG islands are methylated in the promoter of a gene this can reduce or silence gene transcription.<ref name="pmid11782440">{{cite journal |vauthors=Bird A |title=DNA methylation patterns and epigenetic memory |journal=Genes Dev |volume=16 |issue=1 |pages=6–21 |date=January 2002 |pmid=11782440 |doi=10.1101/gad.947102 |url=|doi-access=free }}</ref>

[[DNA methylation]] regulates gene transcription through interaction with methyl binding domain (MBD) proteins, such as MeCP2, MBD1 and MBD2. These [[Methyl-CpG-binding domain|MBD]] proteins bind most strongly to highly methylated [[CpG site#CpG islands|CpG islands]].<ref name=Du>{{cite journal |vauthors=Du Q, Luu PL, Stirzaker C, Clark SJ |title=Methyl-CpG-binding domain proteins: readers of the epigenome |journal=Epigenomics |volume=7 |issue=6 |pages=1051–73 |date=2015 |pmid=25927341 |doi=10.2217/epi.15.39 |url=|doi-access=free }}</ref> These MBD proteins have both a methyl-CpG-binding domain as well as a transcription repression domain.<ref name=Du /> They bind to methylated DNA and guide or direct protein complexes with chromatin remodeling and/or histone modifying activity to methylated CpG islands. MBD proteins generally repress local chromatin such as by catalyzing the introduction of repressive histone marks, or creating an overall repressive chromatin environment through nucleosome remodeling and chromatin reorganization.<ref name=Du />
[[File:Human karyotype with bands and sub-bands.png|thumb|Schematic [[karyotype|karyogram]] of a human, showing an overview of the [[human genome]] on [[G banding]], wherein the lighter regions are generally more transcriptionally active, whereas darker regions are more inactive, including [[non-coding DNA]].{{further|Karyotype}}]]
As noted in the previous section, [[transcription factors]] are proteins that bind to specific DNA sequences in order to regulate the expression of a gene. The binding sequence for a transcription factor in DNA is usually about 10 or 11 nucleotides long. As summarized in 2009, Vaquerizas et al. indicated there are approximately 1,400 different transcription factors encoded in the human genome by genes that constitute about 6% of all human protein encoding genes.<ref name="pmid19274049">{{cite journal |vauthors=Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM |title=A census of human transcription factors: function, expression and evolution |journal=Nat. Rev. Genet. |volume=10 |issue=4 |pages=252–63 |date=April 2009 |pmid=19274049 |doi=10.1038/nrg2538 |s2cid=3207586 }}</ref> About 94% of transcription factor binding sites (TFBSs) that are associated with signal-responsive genes occur in enhancers while only about 6% of such TFBSs occur in promoters.<ref name="pmid29987030"/>

[[EGR1]] protein is a particular transcription factor that is important for regulation of methylation of CpG islands. An [[EGR1]] transcription factor binding site is frequently located in enhancer or promoter sequences.<ref name=SunZ>{{cite journal |vauthors=Sun Z, Xu X, He J, Murray A, Sun MA, Wei X, Wang X, McCoig E, Xie E, Jiang X, Li L, Zhu J, Chen J, Morozov A, Pickrell AM, Theus MH, Xie H |title=EGR1 recruits TET1 to shape the brain methylome during development and upon neuronal activity |journal=Nat Commun |volume=10 |issue=1 |pages=3892 |date=August 2019 |pmid=31467272 |pmc=6715719 |doi=10.1038/s41467-019-11905-3 |bibcode=2019NatCo..10.3892S |url=}}</ref> There are about 12,000 binding sites for EGR1 in the mammalian genome and about half of EGR1 binding sites are located in promoters and half in enhancers.<ref name=SunZ /> The binding of EGR1 to its target DNA binding site is insensitive to cytosine methylation in the DNA.<ref name=SunZ />

While only small amounts of EGR1 transcription factor protein are detectable in cells that are un-stimulated, translation of the ''EGR1'' gene into protein at one hour after stimulation is drastically elevated.<ref name=Kubosaki>{{cite journal |vauthors=Kubosaki A, Tomaru Y, Tagami M, Arner E, Miura H, Suzuki T, Suzuki M, Suzuki H, Hayashizaki Y |title=Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation |journal=Genome Biol |volume=10 |issue=4 |pages=R41 |date=2009 |pmid=19374776 |pmc=2688932 |doi=10.1186/gb-2009-10-4-r41 |url= |doi-access=free }}</ref> Production of EGR1 transcription factor proteins, in various types of cells, can be stimulated by growth factors, neurotransmitters, hormones, stress and injury.<ref name=Kubosaki /> In the brain, when neurons are activated, EGR1 proteins are up-regulated and they bind to (recruit) the pre-existing [[TET enzymes|TET1]] enzymes that are produced in high amounts in neurons. [[TET enzymes]] can catalyse demethylation of 5-methylcytosine. When EGR1 transcription factors bring TET1 enzymes to EGR1 binding sites in promoters, the TET enzymes can [[DNA demethylation|demethylate]] the methylated CpG islands at those promoters. Upon demethylation, these promoters can then initiate transcription of their target genes. Hundreds of genes in neurons are differentially expressed after neuron activation through EGR1 recruitment of TET1 to methylated regulatory sequences in their promoters.<ref name=SunZ />

The methylation of promoters is also altered in response to signals. The three mammalian [[DNA methyltransferase#Mammalian|DNA methyltransferases]]s (DNMT1, DNMT3A, and DNMT3B) catalyze the addition of methyl groups to cytosines in DNA. While DNMT1 is a maintenance methyltransferase, DNMT3A and DNMT3B can carry out new methylations. There are also two [[Alternative splicing|splice]] [[protein isoform]]s produced from the ''DNMT3A'' gene: DNA methyltransferase proteins DNMT3A1 and DNMT3A2.<ref name="pmid28513272">{{cite journal |vauthors=Bayraktar G, Kreutz MR |title=Neuronal DNA Methyltransferases: Epigenetic Mediators between Synaptic Activity and Gene Expression? |journal=Neuroscientist |volume=24 |issue=2 |pages=171–185 |date=April 2018 |pmid=28513272 |pmc=5846851 |doi=10.1177/1073858417707457 |url=}}</ref>

The splice isoform DNMT3A2 behaves like the product of a classical immediate-early gene and, for instance, it is robustly and transiently produced after neuronal activation.<ref name="pmid22751036">{{cite journal |vauthors=Oliveira AM, Hemstedt TJ, Bading H |title=Rescue of aging-associated decline in Dnmt3a2 expression restores cognitive abilities |journal=Nat Neurosci |volume=15 |issue=8 |pages=1111–3 |date=July 2012 |pmid=22751036 |doi=10.1038/nn.3151 |s2cid=10590208 |url=}}</ref> Where the DNA methyltransferase isoform DNMT3A2 binds and adds methyl groups to cytosines appears to be determined by histone post translational modifications.<ref name="pmid20547484">{{cite journal |vauthors=Dhayalan A, Rajavelu A, Rathert P, Tamas R, Jurkowska RZ, Ragozin S, Jeltsch A |title=The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation |journal=J Biol Chem |volume=285 |issue=34 |pages=26114–20 |date=August 2010 |pmid=20547484 |pmc=2924014 |doi=10.1074/jbc.M109.089433 |url=|doi-access=free }}</ref><ref name="pmid29074627">{{cite journal |vauthors=Manzo M, Wirz J, Ambrosi C, Villaseñor R, Roschitzki B, Baubec T |title=Isoform-specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands |journal=EMBO J |volume=36 |issue=23 |pages=3421–34 |date=December 2017 |pmid=29074627 |pmc=5709737 |doi=10.15252/embj.201797038 |url=}}</ref><ref name="pmid31634469">{{cite journal |vauthors=Dukatz M, Holzer K, Choudalakis M, Emperle M, Lungu C, Bashtrykov P, Jeltsch A |title=H3K36me2/3 Binding and DNA Binding of the DNA Methyltransferase DNMT3A PWWP Domain Both Contribute to its Chromatin Interaction |journal=J Mol Biol |volume=431 |issue=24 |pages=5063–74 |date=December 2019 |pmid=31634469 |doi=10.1016/j.jmb.2019.09.006 |s2cid=204832601 |url=}}</ref>

On the other hand, neural activation causes degradation of DNMT3A1 accompanied by reduced methylation of at least one evaluated targeted promoter.<ref name="pmid32726795">{{cite journal |vauthors=Bayraktar G, Yuanxiang P, Confettura AD, Gomes GM, Raza SA, Stork O, Tajima S, Suetake I, Karpova A, Yildirim F, Kreutz MR |title=Synaptic control of DNA methylation involves activity-dependent degradation of DNMT3A1 in the nucleus |journal=Neuropsychopharmacology |volume=45 |issue=12 |pages=2120–30 |date=November 2020 |pmid=32726795 |pmc=7547096 |doi=10.1038/s41386-020-0780-2 |url=}}</ref>