Editing Transcription (biology) (section)

== Major steps ==
{{further|Bacterial transcription|Eukaryotic transcription}}

Transcription is divided into ''initiation'', ''promoter escape'', ''elongation,'' and ''termination''.<ref name="MBOG">{{cite book |vauthors=Watson JD, Baker TA, Bell SP, Gann AA, Levine M, Losick RM | title=Molecular Biology of the Gene | publisher=Pearson | edition=7th | year=2013 |isbn=978-0-321-76243-6 |oclc=0321762436}}</ref>

===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>

=== Initiation ===
{{Multiple image
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| image1            = Transcription initiation eukaryote A.svg
| caption1          = The regulatory sequence elements (yellow) at the start of a eukaryotic protein-coding gene, can be immediately upstream of the open read frame (ORF, red), or many kilobases away (upstream or downstream). Promoter and enhancer regions up-regulate (and silencers downregulate) transcription from DNA to mRNA. The 5' and 3' untranslated regions of that mRNA (UTR, blue) then regulate translation into the final protein product.<ref name="10.26826/1017">{{Cite book |last1=Pakay |first1=Julian |title=Threshold Concepts in Biochemistry |last2=Duivenvoorden |first2=Hendrika |last3=Shafee |first3=Thomas |last4=Clarke |first4=Kaitlin |publisher=La Trobe eBureau |year=2023 |isbn=978-0-6484681-9-6 |doi=10.26826/1017|s2cid=258899183 }}</ref>
| image2            = Transcription initiation eukaryote B.svg
| caption2          = During transcription initiation, proteins (dark grey semi-circles) bound to the DNA can be brought into proximity with each other since the intervening DNA can loop back on itself. In this way, the basal transcription machinery can interact with distant activators and repressors many kilobases upstream or downstream of the open reading frame.<ref name="10.26826/1017"/>
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Transcription begins with the RNA polymerase and one or more [[transcription factor|general transcription factors]] binding to a DNA [[Promoter (genetics)|promoter]] sequence to form an RNA polymerase-promoter closed complex. In the closed complex, the promoter DNA is still fully double-stranded.<ref name="MBOG"/>

RNA polymerase, assisted by one or more general transcription factors, then unwinds approximately 14 base pairs of DNA to form an RNA polymerase-promoter open complex. In the open complex, the promoter DNA is partly unwound and single-stranded. The exposed, single-stranded DNA is referred to as the "[[transcription bubble]]".<ref name="MBOG"/>

RNA polymerase, assisted by one or more general transcription factors, then selects a '''transcription start site''' in the transcription bubble, binds to an initiating [[Nucleoside triphosphate|NTP]] and an extending [[Nucleoside triphosphate|NTP]] (or a short RNA [[Primer (molecular biology)|primer]] and an extending NTP) complementary to the transcription start site sequence, and catalyzes bond formation to yield an initial RNA product.<ref name="MBOG"/>

In [[bacteria]], RNA polymerase [[holoenzyme]] consists of five subunits: 2 α subunits, 1 β subunit, 1 β' subunit, and 1 ω subunit. In bacteria, there is one general RNA transcription factor known as a [[sigma factor]]. RNA polymerase core enzyme binds to the bacterial general transcription (sigma) factor to form RNA polymerase holoenzyme and then binds to a promoter.<ref name="MBOG"/>
(RNA polymerase is called a holoenzyme when sigma subunit is attached to the core enzyme which is consist of 2 α subunits, 1 β subunit, 1 β' subunit only). Unlike eukaryotes, the initiating nucleotide of nascent bacterial mRNA is not capped with a modified guanine nucleotide. The initiating nucleotide of bacterial transcripts bears a 5′ triphosphate (5′-PPP), which can be used for genome-wide mapping of transcription initiation sites.<ref name="Boutard2016">{{cite journal|last1=Boutard|first1=Magali|title=Global repositioning of transcription start sites in a plant-fermenting bacterium|journal=Nature Communications|volume=7|year=2016|page=13783|doi=10.1038/ncomms13783|pmid=27982035|pmc=5171806|bibcode=2016NatCo...713783B|doi-access=free}}</ref>

In [[archaea]] and [[eukaryotes]], RNA polymerase contains subunits [[Sequence homology|homologous]] to each of the five RNA polymerase subunits in bacteria and also contains additional subunits. In archaea and eukaryotes, the functions of the bacterial general transcription factor sigma are performed by multiple general transcription factors that work together.<ref name="MBOG"/> In archaea, there are three general transcription factors: [[TATA-binding protein|TBP]], [[Archaeal transcription factor B|TFB]], and [[2,2,2-Trifluoroethanol|TFE]]. In eukaryotes, in [[RNA polymerase II]]-dependent transcription, there are six general transcription factors: [[TFIIA]], [[TFIIB]] (an [[orthologous|ortholog]] of archaeal TFB), [[TFIID]] (a multisubunit factor in which the key subunit, [[TATA-binding protein|TBP]], is an [[orthologous|ortholog]] of archaeal TBP), [[TFIIE]] (an [[orthologous|ortholog]] of archaeal TFE), [[TFIIF]], and [[TFIIH]]. The TFIID is the first component to bind to DNA due to binding of TBP, while TFIIH is the last component to be recruited. In archaea and eukaryotes, the RNA polymerase-promoter closed complex is usually referred to as the "[[Transcription preinitiation complex|preinitiation complex]]".<ref name="Roeder1991">{{cite journal|last1=Roeder|first1=Robert G.|title=The complexities of eukaryotic transcription initiation: regulation of preinitiation complex assembly|journal=Trends in Biochemical Sciences|volume=16|year=1991|issue=11|pages=402–8 |doi=10.1016/0968-0004(91)90164-Q|pmid=1776168}}</ref>

Transcription initiation is regulated by additional proteins, known as [[activator (genetics)|activators]] and [[repressor]]s, and, in some cases, associated [[coactivator]]s or [[coactivator|corepressors]], which modulate formation and function of the transcription initiation complex.<ref name="MBOG"/>

{{anchor|Promoter clearance}}

=== Promoter escape ===

After the first bond is synthesized, the RNA polymerase must escape the promoter. During this time there is a tendency to release the RNA transcript and produce truncated transcripts. This is called [[abortive initiation]], and is common for both eukaryotes and prokaryotes.<ref>{{cite journal | vauthors = Goldman SR, Ebright RH, Nickels BE | title = Direct detection of abortive RNA transcripts in vivo | journal = Science | volume = 324 | issue = 5929 | pages = 927–8 | date = May 2009 | pmid = 19443781 | pmc = 2718712 | doi = 10.1126/science.1169237 | bibcode = 2009Sci...324..927G | author-link2 = Richard H. Ebright }}</ref> Abortive initiation continues to occur until an RNA product of a threshold length of approximately 10 nucleotides is synthesized, at which point promoter escape occurs and a transcription elongation complex is formed.{{citation needed|date=April 2023}}

Mechanistically, promoter escape occurs through [[DNA scrunching]], providing the energy needed to break interactions between RNA polymerase holoenzyme and the promoter.<ref>{{cite journal | vauthors = Revyakin A, Liu C, Ebright RH, Strick TR | title = Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching | journal = Science | volume = 314 | issue = 5802 | pages = 1139–43 | date = November 2006 | pmid = 17110577 | pmc = 2754787 | doi = 10.1126/science.1131398 | bibcode = 2006Sci...314.1139R }}</ref>

In bacteria, it was historically thought that the [[sigma factor]] is definitely released after promoter clearance occurs. This theory had been known as the ''obligate release model.'' However, later data showed that upon and following promoter clearance, the sigma factor is released according to a [[stochastic process|stochastic model]] known as the ''stochastic release model''.<ref>{{cite journal | vauthors = Raffaelle M, Kanin EI, Vogt J, Burgess RR, Ansari AZ | title = Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo | journal = Molecular Cell | volume = 20 | issue = 3 | pages = 357–66 | date = November 2005 | pmid = 16285918 | doi = 10.1016/j.molcel.2005.10.011 | doi-access = free }}</ref>

In eukaryotes, at an RNA polymerase II-dependent promoter, upon promoter clearance, TFIIH phosphorylates serine 5 on the carboxy terminal domain of RNA polymerase II, leading to the recruitment of capping enzyme (CE).<ref>{{cite journal | vauthors = Mandal SS, Chu C, Wada T, Handa H, Shatkin AJ, Reinberg D | title = Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 101 | issue = 20 | pages = 7572–7 | date = May 2004 | pmid = 15136722 | pmc = 419647 | doi = 10.1073/pnas.0401493101 | bibcode = 2004PNAS..101.7572M | doi-access = free }}</ref><ref>{{cite journal | vauthors = Goodrich JA, Tjian R | title = Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II | journal = Cell | volume = 77 | issue = 1 | pages = 145–56 | date = April 1994 | pmid = 8156590 | doi = 10.1016/0092-8674(94)90242-9 | s2cid = 24602504 }}</ref> The exact mechanism of how CE induces promoter clearance in eukaryotes is not yet known.

=== Elongation ===
[[File:Simple transcription elongation1.svg|thumb|400px|Simple diagram of transcription elongation]]

One strand of the DNA, the ''template strand'' (or noncoding strand), is used as a template for RNA synthesis. As transcription proceeds, RNA polymerase traverses the template strand and uses base pairing complementarity with the DNA template to create an RNA copy (which elongates during the traversal). Although RNA polymerase traverses the template strand from 3' → 5', the coding (non-template) strand and newly formed RNA can also be used as reference points, so transcription can be described as occurring 5' → 3'. This produces an RNA molecule from 5' → 3', an exact copy of the coding strand (except that [[thymine]]s are replaced with [[uracil]]s, and the nucleotides are composed of a ribose (5-carbon) sugar whereas DNA has deoxyribose (one fewer oxygen atom) in its sugar-phosphate backbone).<ref name="Clark-2005" />

mRNA transcription can involve multiple RNA polymerases on a single DNA template and multiple rounds of transcription (amplification of particular mRNA), so many mRNA molecules can be rapidly produced from a single copy of a gene.{{citation needed|date=January 2011}} The characteristic elongation rates in prokaryotes and eukaryotes are about 10–100 nts/sec.<ref>{{cite book |last1=Milo |first1=Ron |last2=Philips |first2=Rob |chapter=4. Rates and Duration: Central dogma: Which is faster:transcription or translation? |chapter-url= |title=Cell Biology by the Numbers |publisher=CRC Press |date=2015 |isbn=978-1-317-23069-4 |pages=231–6 |url={{GBurl|9NPRCgAAQBAJ|pg=PR10}} |oclc=1105558425 }}</ref> In eukaryotes, however, [[nucleosome]]s act as major barriers to transcribing polymerases during transcription elongation.<ref>{{cite journal | vauthors = Hodges C, Bintu L, Lubkowska L, Kashlev M, Bustamante C | title = Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II | journal = Science | volume = 325 | issue = 5940 | pages = 626–8 | date = July 2009 | pmid = 19644123 | pmc = 2775800 | doi = 10.1126/science.1172926| bibcode = 2009Sci...325..626H }}</ref><ref name="Fitz etal-2016" /> In these organisms, the pausing induced by nucleosomes can be regulated by transcription elongation factors such as TFIIS.<ref name="Fitz etal-2016">{{cite journal |date=2016 |title=Nucleosomal arrangement affects single-molecule transcription dynamics |journal=Proceedings of the National Academy of Sciences |volume=113 |issue=45 |pages=12733–12738 |vauthors=Fitz V, Shin J, Ehrlich C, Farnung L, Cramer P, Zaburdaev V, Grill SW |pmc=5111697 |doi=10.1073/pnas.1602764113 |pmid=27791062|bibcode=2016PNAS..11312733F |doi-access=free }}</ref>

Elongation also involves a proofreading mechanism that can replace incorrectly incorporated bases. In eukaryotes, this may correspond with short pauses during transcription that allow appropriate RNA editing factors to bind. These pauses may be intrinsic to the RNA polymerase or due to chromatin structure.{{citation needed|date=October 2019}}

Double-strand breaks in actively transcribed regions of DNA are repaired by [[homologous recombination]] during the S and G2 phases of the [[cell cycle]].<ref>{{cite journal |vauthors=Aymard F, Bugler B, Schmidt CK, Guillou E, Caron P, Briois S, Iacovoni JS, Daburon V, Miller KM, Jackson SP, Legube G |title=Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks |journal=Nat Struct Mol Biol |volume=21 |issue=4 |pages=366–74 |date=April 2014 |pmid=24658350 |pmc=4300393 |doi=10.1038/nsmb.2796 }}</ref><ref>{{cite journal |vauthors=Ouyang J, Yadav T, Zhang JM, Yang H, Rheinbay E, Guo H, Haber DA, Lan L, Zou L |title=RNA transcripts stimulate homologous recombination by forming DR-loops |journal=Nature |volume=594 |issue=7862 |pages=283–8 |date=June 2021 |pmid=33981036 |pmc=8855348 |doi=10.1038/s41586-021-03538-8 |bibcode=2021Natur.594..283O }}</ref> Since transcription enhances the accessibility of DNA to exogenous chemicals and internal metabolites that can cause recombinogenic lesions, homologous recombination of a particular DNA sequence may be strongly stimulated by transcription.<ref>{{cite journal |vauthors=García-Rubio M, Huertas P, González-Barrera S, Aguilera A |title=Recombinogenic effects of DNA-damaging agents are synergistically increased by transcription in Saccharomyces cerevisiae. New insights into transcription-associated recombination |journal=Genetics |volume=165 |issue=2 |pages=457–66 |date=October 2003 |pmid=14573461 |pmc=1462770 |doi=10.1093/genetics/165.2.457 }}</ref>

=== Termination ===
{{main|Terminator (genetics)}}

Bacteria use two different strategies for transcription termination – Rho-independent termination and Rho-dependent termination. In [[Rho-independent transcription termination]], RNA transcription stops when the newly synthesized RNA molecule forms a G-C-rich [[hairpin loop]] followed by a run of Us. When the hairpin forms, the mechanical stress breaks the weak rU-dA bonds, now filling the DNA–RNA hybrid. This pulls the poly-U transcript out of the active site of the RNA polymerase, terminating transcription. In Rho-dependent termination, [[Rho factor|Rho]], a protein factor, destabilizes the interaction between the template and the mRNA, thus releasing the newly synthesized mRNA from the elongation complex.<ref>{{cite journal | vauthors = Richardson JP | title = Rho-dependent termination and ATPases in transcript termination | journal = Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression | volume = 1577 | issue = 2 | pages = 251–260 | date = September 2002 | pmid = 12213656 | doi = 10.1016/S0167-4781(02)00456-6 }}</ref>

Transcription termination in eukaryotes is less well understood than in bacteria, but involves cleavage of the new transcript followed by template-independent addition of adenines at its new 3' end, in a process called [[polyadenylation]].<ref>{{cite journal | vauthors = Lykke-Andersen S, Jensen TH | title = Overlapping pathways dictate termination of RNA polymerase II transcription | journal = Biochimie | volume = 89 | issue = 10 | pages = 1177–82 | date = October 2007 | pmid = 17629387 | doi = 10.1016/j.biochi.2007.05.007 }}</ref>

Beyond termination by a terminator sequences (which is a part of a [[gene]]), transcription may also need to be terminated when it encounters conditions such as DNA damage or an active [[replication fork]]. In bacteria, the [[Mutation Frequency Decline|Mfd]] ATPase can remove a RNA polymerase stalled at a lesion by prying open its clamp. It also recruits [[nucleotide excision repair]] machinery to repair the lesion. Mfd is proposed to also resolve conflicts between DNA replication and transcription.<ref>{{cite journal |last1=Shi |first1=J |last2=Wen |first2=A |last3=Zhao |first3=M |last4=Jin |first4=S |last5=You |first5=L |last6=Shi |first6=Y |last7=Dong |first7=S |last8=Hua |first8=X |last9=Zhang |first9=Y |last10=Feng |first10=Y |title=Structural basis of Mfd-dependent transcription termination. |journal=Nucleic Acids Research |date=18 November 2020 |volume=48 |issue=20 |pages=11762–11772 |doi=10.1093/nar/gkaa904 |pmid=33068413|doi-access=free |pmc=7672476 }}</ref> In eukayrotes, ATPase [[TTF2]] helps to suppress the action of RNAP I and II during [[mitosis]], preventing errors in chromosomal segregation.<ref>{{cite journal |last1=Jiang |first1=Y |last2=Liu |first2=M |last3=Spencer |first3=CA |last4=Price |first4=DH |title=Involvement of transcription termination factor 2 in mitotic repression of transcription elongation. |journal=Molecular Cell |date=7 May 2004 |volume=14 |issue=3 |pages=375–85 |doi=10.1016/s1097-2765(04)00234-5 |pmid=15125840|doi-access=free }}</ref> In archaea, the Eta ATPase is proposed to play a similar role.<ref>{{cite journal |last1=Marshall |first1=CJ |last2=Qayyum |first2=MZ |last3=Walker |first3=JE |last4=Murakami |first4=KS |last5=Santangelo |first5=TJ |title=The structure and activities of the archaeal transcription termination factor Eta detail vulnerabilities of the transcription elongation complex. |journal=Proceedings of the National Academy of Sciences of the United States of America |date=9 August 2022 |volume=119 |issue=32 |pages=e2207581119 |doi=10.1073/pnas.2207581119 |pmid=35917344|doi-access=free |pmc=9371683 |bibcode=2022PNAS..11907581M }}</ref>

===Transcription increases susceptibility to DNA damage===

Genome damage occurs with a high frequency, estimated to range between tens and hundreds of thousands of DNA damages arising in each cell every day.<ref name = Milano2023>{{cite journal |vauthors=Milano L, Gautam A, Caldecott KW |title=DNA damage and transcription stress |journal=Mol Cell |volume=84 |issue=1 |pages=70–79 |date=January 2024 |pmid=38103560 |doi=10.1016/j.molcel.2023.11.014 |url=}}</ref>  The process of transcription is a major source of DNA damage, due to the formation of single-strand DNA intermediates that are vulnerable to damage.<ref name = Milano2023/> The regulation of transcription by processes using [[base excision repair]] and/or [[topoisomerase]]s to cut and remodel the genome also increases the vulnerability of DNA to damage.<ref name = Milano2023/>