Editing Transcription (biology) (section)

===Setting up for transcription===
{{cleanup section|reason=Duplication with [[Regulatory sequence]]. Can we just make a canonical "main article" and redirect people there?|date=September 2021}}

====Enhancers, transcription factors, Mediator complex, and DNA loops in mammalian transcription====
[[File:Regulation of transcription in mammals.jpg|thumb|right|upright=2| '''Regulation of transcription in mammals'''. This illustration indicates many of the elements that are present when transcription of a gene is upregulated.]] 
[[Transcription preinitiation complex|Setting up]] for transcription in mammals is regulated by many [[cis-regulatory element]]s, including [[Promoter (genetics)|core promoter and promoter-proximal elements]] that are located near the [[Eukaryotic transcription|transcription start sites]] of genes. Core promoters combined with [[general transcription factor]]s are sufficient to direct transcription initiation, but generally have low basal activity.<ref name="pmid29946135">{{cite journal |vauthors=Haberle V, Stark A |title=Eukaryotic core promoters and the functional basis of transcription initiation |journal=Nat Rev Mol Cell Biol |volume=19 |issue=10 |pages=621–637 |date=October 2018 |pmid=29946135 |pmc=6205604 |doi=10.1038/s41580-018-0028-8 |url=}}</ref> Other important cis-regulatory modules are localized in DNA regions that are distant from the transcription start sites. These include [[Enhancer (genetics)|enhancers]], [[Silencer (genetics)|silencers]], [[Insulator (genetics)|insulators]] and tethering elements.<ref name="pmid33102493">{{cite journal |vauthors=Verheul TC, van Hijfte L, Perenthaler E, Barakat TS |title=The Why of YY1: Mechanisms of Transcriptional Regulation by Yin Yang 1 |journal=Front Cell Dev Biol |volume=8 |issue= |pages=592164 |date=2020 |pmid=33102493 |pmc=7554316 |doi=10.3389/fcell.2020.592164 |url=|doi-access=free }}</ref> Among this constellation of elements, enhancers and their associated [[transcription factors]] have a leading role in the initiation of gene transcription.<ref name="pmid22868264">{{cite journal |vauthors=Spitz F, Furlong EE |title=Transcription factors: from enhancer binding to developmental control |journal=Nat Rev Genet |volume=13 |issue=9 |pages=613–26 |date=September 2012 |pmid=22868264 |doi=10.1038/nrg3207 |s2cid=205485256 |url=}}</ref> An enhancer localized in a DNA region distant from the promoter of a gene can have a very large effect on gene transcription, with some genes undergoing up to 100-fold increased transcription due to an activated enhancer.<ref name=Beagan>{{cite journal |vauthors=Beagan JA, Pastuzyn ED, Fernandez LR, Guo MH, Feng K, Titus KR, Chandrashekar H, Shepherd JD, Phillips-Cremins JE |title=Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression |journal=Nat Neurosci |volume=23 |issue=6 |pages=707–717 |date=June 2020 |pmid=32451484 |pmc=7558717 |doi=10.1038/s41593-020-0634-6 |url=}}</ref>

Enhancers are regions of the genome that are major gene-regulatory elements. Enhancers control cell-type-specific gene transcription programs, most often by looping through long distances to come in physical proximity with the promoters of their target genes.<ref name=Schoenfelder>{{cite journal |vauthors=Schoenfelder S, Fraser P |title=Long-range enhancer-promoter contacts in gene expression control |journal=Nat Rev Genet |volume=20 |issue=8 |pages=437–455 |date=August 2019 |pmid=31086298 |doi=10.1038/s41576-019-0128-0 |s2cid=152283312 |url=}}</ref> While there are hundreds of thousands of enhancer DNA regions,<ref name="pmid23503198">{{cite journal |vauthors=Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G |title=Enhancers: five essential questions |journal=Nat Rev Genet |volume=14 |issue=4 |pages=288–95 |date=April 2013 |pmid=23503198 |pmc=4445073 |doi=10.1038/nrg3458 |url=}}</ref> for a particular type of tissue only specific enhancers are brought into proximity with the promoters that they regulate. In a study of brain cortical neurons, 24,937 loops were found, bringing enhancers to their target promoters.<ref name=Beagan /> Multiple enhancers, each often at tens or hundred of thousands of nucleotides distant from their target genes, loop to their target gene promoters and can coordinate with each other to control transcription of their common target gene.<ref name=Schoenfelder />

The schematic illustration in this section shows an enhancer looping around to come into close physical proximity with the promoter of a target gene. The loop is stabilized by a dimer of a connector protein (e.g. dimer of [[CTCF]] or [[YY1]]), with one member of the dimer anchored to its binding motif on the enhancer and the other member anchored to its binding motif on the promoter (represented by the red zigzags in the illustration).<ref name="pmid29224777">{{cite journal |vauthors=Weintraub AS, Li CH, Zamudio AV, Sigova AA, Hannett NM, Day DS, Abraham BJ, Cohen MA, Nabet B, Buckley DL, Guo YE, Hnisz D, Jaenisch R, Bradner JE, Gray NS, Young RA |title=YY1 Is a Structural Regulator of Enhancer-Promoter Loops |journal=Cell |volume=171 |issue=7 |pages=1573–88.e28 |date=December 2017 |pmid=29224777 |pmc=5785279 |doi=10.1016/j.cell.2017.11.008 |url=}}</ref> Several cell function specific transcription factors (there are about 1,600 transcription factors in a human cell<ref name="pmid29425488">{{cite journal |vauthors=Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT |title=The Human Transcription Factors |journal=Cell |volume=172 |issue=4 |pages=650–665 |date=February 2018 |pmid=29425488 |doi=10.1016/j.cell.2018.01.029 |url=|doi-access=free }}</ref>) generally bind to specific motifs on an enhancer<ref name="pmid29987030">{{cite journal |vauthors=Grossman SR, Engreitz J, Ray JP, Nguyen TH, Hacohen N, Lander ES |title=Positional specificity of different transcription factor classes within enhancers |journal=Proc Natl Acad Sci U S A |volume=115 |issue=30 |pages=E7222–30 |date=July 2018 |pmid=29987030 |pmc=6065035 |doi=10.1073/pnas.1804663115 |bibcode=2018PNAS..115E7222G |url=|doi-access=free }}</ref> and a small combination of these enhancer-bound transcription factors, when brought close to a promoter by a DNA loop, govern level of transcription of the target gene. [[Mediator (coactivator)|Mediator]] (a complex usually consisting of about 26 proteins in an interacting structure) communicates regulatory signals from enhancer DNA-bound transcription factors directly to the RNA polymerase II (pol II) enzyme bound to the promoter.<ref name="pmid25693131">{{cite journal |vauthors=Allen BL, Taatjes DJ |title=The Mediator complex: a central integrator of transcription |journal=Nat Rev Mol Cell Biol |volume=16 |issue=3 |pages=155–66 |date=March 2015 |pmid=25693131 |pmc=4963239 |doi=10.1038/nrm3951 |url=}}</ref>

Enhancers, when active, are generally transcribed from both strands of DNA with RNA polymerases acting in two different directions, producing two [[enhancer RNA]]s (eRNAs) as illustrated in the Figure.<ref name="pmid29378788">{{cite journal |vauthors=Mikhaylichenko O, Bondarenko V, Harnett D, Schor IE, Males M, Viales RR, Furlong EE |title=The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription |journal=Genes Dev |volume=32 |issue=1 |pages=42–57 |date=January 2018 |pmid=29378788 |pmc=5828394 |doi=10.1101/gad.308619.117 |url=}}</ref> An inactive enhancer may be bound by an inactive transcription factor. Phosphorylation of the transcription factor may activate it and that activated transcription factor may then activate the enhancer to which it is bound (see small red star representing phosphorylation of transcription factor bound to enhancer in the illustration).<ref name="pmid12514134">{{cite journal |vauthors=Li QJ, Yang SH, Maeda Y, Sladek FM, Sharrocks AD, Martins-Green M |title=MAP kinase phosphorylation-dependent activation of Elk-1 leads to activation of the co-activator p300 |journal=EMBO J |volume=22 |issue=2 |pages=281–91 |date=January 2003 |pmid=12514134 |pmc=140103 |doi=10.1093/emboj/cdg028 |url=}}</ref> An activated enhancer begins transcription of its RNA before activating transcription of messenger RNA from its target gene.<ref name="pmid32810208">{{cite journal |vauthors=Carullo NV, Phillips I RA, Simon RC, Soto SA, Hinds JE, Salisbury AJ, Revanna JS, Bunner KD, Ianov L, Sultan FA, Savell KE, Gersbach CA, Day JJ |title=Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems |journal=Nucleic Acids Res |volume=48 |issue=17 |pages=9550–70 |date=September 2020 |pmid=32810208 |pmc=7515708 |doi=10.1093/nar/gkaa671 |url=}}</ref>

====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>