Transcriptional regulation

File:Maltose Operon Without Maltose Present.png of the maltose genes will occur, and there is no maltose to bind to the maltose activator protein. This prevents the activator protein from binding to the activator binding site on the gene, which in turn prevents RNA polymerase from binding to the maltose promoter. No transcription takes place.]]

Much of the early understanding of transcription came from bacteria,{{cite journal | vauthors = JACOB F, MONOD J | title = Genetic regulatory mechanisms in the synthesis of proteins | journal = J. Mol. Biol. | volume = 3 | issue = 3| pages = 318–56 | date = June 1961 | pmid = 13718526 | doi = 10.1016/s0022-2836(61)80072-7| s2cid = 19804795 }} although the extent and complexity of transcriptional regulation is greater in eukaryotes. Bacterial transcription is governed by three main sequence elements:

• Promoters are elements of DNA that may bind RNA polymerase and other proteins for the successful initiation of transcription directly upstream of the gene.
• Operators recognize repressor proteins that bind to a stretch of DNA and inhibit the transcription of the gene.
• Positive control elements that bind to DNA and incite higher levels of transcription.{{cite journal | vauthors = Englesberg E, Irr J, Power J, Lee N | title = Positive control of enzyme synthesis by gene C in the L-arabinose system | journal = J. Bacteriol. | volume = 90 | issue = 4 | pages = 946–57 | date = October 1965 | doi = 10.1128/JB.90.4.946-957.1965 | pmid = 5321403 | pmc = 315760 }}

While these means of transcriptional regulation also exist in eukaryotes, the transcriptional landscape is significantly more complicated both by the number of proteins involved as well as by the presence of introns and the packaging of DNA into histones.

The transcription of a basic bacterial gene is dependent on the strength of its promoter and the presence of activators or repressors. In the absence of other regulatory elements, a promoter's sequence-based affinity for RNA polymerases varies, which results in the production of different amounts of transcript. The variable affinity of RNA polymerase for different promoter sequences is related to regions of consensus sequence upstream of the transcription start site. The more nucleotides of a promoter that agree with the consensus sequence, the stronger the affinity of the promoter for RNA Polymerase likely is.{{cite journal | vauthors = Busby S, Ebright RH | title = Promoter structure, promoter recognition, and transcription activation in prokaryotes | journal = Cell | volume = 79 | issue = 5 | pages = 743–6 | date = December 1994 | pmid = 8001112 | doi = 10.1016/0092-8674(94)90063-9 | s2cid = 34940548 }}

File:Maltose Operon With Maltose Present.png is present in E. coli, it binds to the maltose activator protein (#1), which promotes maltose activator protein binding to the activator binding site (#2). This allows the RNA polymerase to bind to the mal promoter (#3). Transcription of malE, malF, and malG genes then proceeds (#4) as maltose activator protein and RNA polymerase moves down the DNA. malE encodes for maltose-binding periplasmic protein and helps maltose transport across the cell membrane.{{Cite web|url=https://www.uniprot.org/uniprot/P0AEX9|title=malE - Maltose-binding periplasmic protein precursor - Escherichia coli (strain K12) - malE gene & protein|website=www.uniprot.org|language=en|access-date=2017-11-20}} malF encodes for maltose transport system permease protein and helps translocate maltose across the cell membrane.{{Cite web|url=https://www.uniprot.org/uniprot/P02916|title=malF - Maltose transport system permease protein MalF - Escherichia coli (strain K12) - malF gene & protein|website=www.uniprot.org|language=en|access-date=2017-11-20}} malG encodes for transport system protein and also helps translocate maltose across the cell membrane.{{Cite web|url=https://www.uniprot.org/uniprot/P68183|title=malG - Maltose transport system permease protein MalG - Escherichia coli (strain K12) - malG gene & protein|website=www.uniprot.org|language=en|access-date=2017-11-20}}]]

In the absence of other regulatory elements, the default state of a bacterial transcript is to be in the “on” configuration, resulting in the production of some amount of transcript. This means that transcriptional regulation in the form of protein repressors and positive control elements can either increase or decrease transcription. Repressors often physically occupy the promoter location, occluding RNA polymerase from binding. Alternatively a repressor and polymerase may bind to the DNA at the same time with a physical interaction between the repressor preventing the opening of the DNA for access to the minus strand for transcription. This strategy of control is distinct from eukaryotic transcription, whose basal state is to be off and where co-factors required for transcription initiation are highly gene dependent.{{cite journal | vauthors = Payankaulam S, Li LM, Arnosti DN | title = Transcriptional repression: conserved and evolved features | journal = Curr. Biol. | volume = 20 | issue = 17 | pages = R764–71 | date = September 2010 | pmid = 20833321 | pmc = 3033598 | doi = 10.1016/j.cub.2010.06.037 | bibcode = 2010CBio...20.R764P }}

Sigma factors are specialized bacterial proteins that bind to RNA polymerases and orchestrate transcription initiation. Sigma factors act as mediators of sequence-specific transcription, such that a single sigma factor can be used for transcription of all housekeeping genes or a suite of genes the cell wishes to express in response to some external stimuli such as stress.{{cite journal | vauthors = Gruber TM, Gross CA | title = Multiple sigma subunits and the partitioning of bacterial transcription space | journal = Annu. Rev. Microbiol. | volume = 57 | pages = 441–66 | date = 2003 | pmid = 14527287 | doi = 10.1146/annurev.micro.57.030502.090913 }}

In addition to processes that regulate transcription at the stage of initiation, mRNA synthesis is also controlled by the rate of transcription elongation.{{cite journal |author1=Kang, J. |author2=Mishanina, T. V. |author3=Landick, R.|author4=Darst, S. A. |name-list-style=amp |year=2019 |title=Mechanisms of Transcriptional Pausing in Bacteria. |journal=Journal of Molecular Biology |volume=431 |issue=20 |pages=4007–4029 |doi = 10.1016/j.jmb.2019.07.017 |pmid=31310765 |pmc=6874753 |doi-access=free }} RNA polymerase pauses occur frequently and are regulated by transcription factors, such as NusG and NusA, transcription-translation coupling, and mRNA secondary structure.{{cite journal |author1=Zhang, J. |author2=Landick, R. |name-list-style=amp |year=2016 |title=A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure. |journal=Journal of Molecular Biology |volume=41 |issue=4 |pages=293–310 |doi = 10.1016/j.tibs.2015.12.009 |pmid=26822487 |pmc=4911296 }}{{cite journal |author1=Artsimovitch, I. |year=2018 |title=Rebuilding the bridge between transcription and translation. |journal=Molecular Microbiology |volume=108 |issue=5 |pages=467–472 |doi = 10.1111/mmi.13964 |pmid=29608805 |pmc=5980768 |doi-access=free }}

File:Human karyotype with bands and sub-bands.png of a human, showing an overview of the human genome on G banding, which is a method that includes Giemsa staining, wherein the lighter staining regions are generally more transcriptionally active, whereas darker regions are more inactive.{{further|Karyotype}}]]

The added complexity of generating a eukaryotic cell carries with it an increase in the complexity of transcriptional regulation. Eukaryotes have three RNA polymerases, known as Pol I, Pol II, and Pol III. Each polymerase has specific targets and activities, and is regulated by independent mechanisms. There are a number of additional mechanisms through which polymerase activity can be controlled. These mechanisms can be generally grouped into three main areas:

• Control over polymerase access to the gene. This is perhaps the broadest of the three control mechanisms. This includes the functions of histone remodeling enzymes, transcription factors, enhancers and repressors, and many other complexes
• Productive elongation of the RNA transcript. Once polymerase is bound to a promoter, it requires another set of factors to allow it to escape the promoter complex and begin successfully transcribing RNA.
• Termination of the polymerase. A number of factors which have been found to control how and when termination occurs, which will dictate the fate of the RNA transcript.

All three of these systems work in concert to integrate signals from the cell and change the transcriptional program accordingly.

While in prokaryotic systems the basal transcription state can be thought of as nonrestrictive (that is, “on” in the absence of modifying factors), eukaryotes have a restrictive basal state which requires the recruitment of other factors in order to generate RNA transcripts. This difference is largely due to the compaction of the eukaryotic genome by winding DNA around histones to form higher order structures. This compaction makes the gene promoter inaccessible without the assistance of other factors in the nucleus, and thus chromatin structure is a common site of regulation. Similar to the sigma factors in prokaryotes, the general transcription factors (GTFs) are a set of factors in eukaryotes that are required for all transcription events. These factors are responsible for stabilizing binding interactions and opening the DNA helix to allow the RNA polymerase to access the template, but generally lack specificity for different promoter sites.{{cite journal | vauthors = Struhl K | title = Fundamentally different logic of gene regulation in eukaryotes and prokaryotes | journal = Cell | volume = 98 | issue = 1 | pages = 1–4 | date = July 1999 | pmid = 10412974 | doi = 10.1016/S0092-8674(00)80599-1 | s2cid = 12411218 | doi-access = free }} A large part of gene regulation occurs through transcription factors that either recruit or inhibit the binding of the general transcription machinery and/or the polymerase. This can be accomplished through close interactions with core promoter elements, or through the long distance enhancer elements.

Once a polymerase is successfully bound to a DNA template, it often requires the assistance of other proteins in order to leave the stable promoter complex and begin elongating the nascent RNA strand. This process is called promoter escape, and is another step at which regulatory elements can act to accelerate or slow the transcription process. Similarly, protein and nucleic acid factors can associate with the elongation complex and modulate the rate at which the polymerase moves along the DNA template.

In eukaryotes, genomic DNA is highly compacted in order to be able to fit it into the nucleus. This is accomplished by winding the DNA around protein octamers called histones, which has consequences for the physical accessibility of parts of the genome at any given time. Significant portions are silenced through histone modifications, and thus are inaccessible to the polymerases or their cofactors. The highest level of transcription regulation occurs through the rearrangement of histones in order to expose or sequester genes, because these processes have the ability to render entire regions of a chromosome inaccessible such as what occurs in imprinting.

Histone rearrangement is facilitated by post-translational modifications to the tails of the core histones. A wide variety of modifications can be made by enzymes such as the histone acetyltransferases (HATs), histone methyltransferases (HMTs), and histone deacetylases (HDACs), among others. These enzymes can add or remove covalent modifications such as methyl groups, acetyl groups, phosphates, and ubiquitin. Histone modifications serve to recruit other proteins which can either increase the compaction of the chromatin and sequester promoter elements, or to increase the spacing between histones and allow the association of transcription factors or polymerase on open DNA.{{cite journal | vauthors = Calo E, Wysocka J | title = Modification of enhancer chromatin: what, how, and why? | journal = Mol. Cell | volume = 49 | issue = 5 | pages = 825–37 | date = March 2013 | pmid = 23473601 | pmc = 3857148 | doi = 10.1016/j.molcel.2013.01.038 }} For example, H3K27 trimethylation by the polycomb complex PRC2 causes chromosomal compaction and gene silencing.{{cite journal | vauthors = de Napoles M, Mermoud JE, Wakao R, Tang YA, Endoh M, Appanah R, Nesterova TB, Silva J, Otte AP, Vidal M, Koseki H, Brockdorff N | title = Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation | journal = Dev. Cell | volume = 7 | issue = 5 | pages = 663–76 | date = November 2004 | pmid = 15525528 | doi = 10.1016/j.devcel.2004.10.005 | doi-access = free }} These histone modifications may be created by the cell, or inherited in an epigenetic fashion from a parent.

File:DNA methylation.svg group to the DNA that happens at cytosine. The image shows a cytosine single ring base and a methyl group added on to the 5 carbon. In mammals, DNA methylation occurs almost exclusively at a cytosine that is followed by a guanine.]]

Transcription regulation at about 60% of promoters is 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 methylated form of the DNA base cytosine (see Figure). 5-mC is an epigenetic marker found predominantly within CpG sites. About 28 million CpG dinucleotides occur in the human genome.{{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=}} In most tissues of mammals, on average, 70% to 80% of CpG cytosines are methylated (forming 5-methylCpG or 5-mCpG).{{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=}} Methylated cytosines within 5’cytosine-guanine 3’ sequences often occur in groups, called CpG islands. About 60% of promoter sequences have a CpG island while only about 6% of enhancer sequences have a CpG island.{{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=5306–5317 |date=June 2020 |pmid=32338759 |pmc=7261191 |doi=10.1093/nar/gkaa223 |url=}} CpG islands constitute regulatory sequences, since if CpG islands are methylated in the promoter of a gene this can reduce or silence gene transcription.{{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 }}

DNA methylation regulates gene transcription through interaction with methyl binding domain (MBD) proteins, such as MeCP2, MBD1 and MBD2. These MBD proteins bind most strongly to highly methylated CpG islands.{{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 }} These MBD proteins have both a methyl-CpG-binding domain as well as a transcription repression domain. 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.

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.{{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 }} 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.

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.{{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=}} 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. The binding of EGR1 to its target DNA binding site is insensitive to cytosine methylation in the DNA.

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.{{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 }} Expression of EGR1 transcription factor proteins, in various types of cells, can be stimulated by growth factors, neurotransmitters, hormones, stress and injury. In the brain, when neurons are activated, EGR1 proteins are up-regulated and they bind to (recruit) the pre-existing TET1 enzymes which are highly expressed 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 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.

The methylation of promoters is also altered in response to signals. The three mammalian DNA methyltransferasess (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 splice protein isoforms produced from the DNMT3A gene: DNA methyltransferase proteins DNMT3A1 and DNMT3A2.{{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=}}

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.{{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=}} Where the DNA methyltransferase isoform DNMT3A2 binds and adds methyl groups to cytosines appears to be determined by histone post translational modifications.{{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 }}{{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=3421–3434 |date=December 2017 |pmid=29074627 |pmc=5709737 |doi=10.15252/embj.201797038 |url=}}{{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=5063–5074 |date=December 2019 |pmid=31634469 |doi=10.1016/j.jmb.2019.09.006 |s2cid=204832601 |url=}}

On the other hand, neural activation causes degradation of DNMT3A1 accompanied by reduced methylation of at least one evaluated targeted promoter.{{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=2120–2130 |date=November 2020 |pmid=32726795 |pmc=7547096 |doi=10.1038/s41386-020-0780-2 |url=}}

Transcription factors are proteins that bind to specific DNA sequences in order to regulate the expression of a given gene. There are approximately 1,400 transcription factors in the human genome and they constitute about 6% of all human protein coding genes. The power of transcription factors resides in their ability to activate and/or repress wide repertoires of downstream target genes. The fact that these transcription factors work in a combinatorial fashion means that only a small subset of an organism's genome encodes transcription factors.

Transcription factors function through a wide variety of mechanisms. In one mechanism, CpG methylation influences binding of most transcription factors to DNA—in some cases negatively and in others positively.{{cite journal |vauthors=Yin Y, Morgunova E, Jolma A, Kaasinen E, Sahu B, Khund-Sayeed S, Das PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schübeler D, Vinson C, Taipale J |title=Impact of cytosine methylation on DNA binding specificities of human transcription factors |journal=Science |volume=356 |issue=6337 |pages= eaaj2239|date=May 2017 |pmid=28473536 |doi=10.1126/science.aaj2239 |s2cid=206653898 |pmc=8009048 }} In addition, often they are at the end of a signal transduction pathway that functions to change something about the factor, like its subcellular localization or its activity. Post-translational modifications to transcription factors located in the cytosol can cause them to translocate to the nucleus where they can interact with their corresponding enhancers. Other transcription factors are already in the nucleus, and are modified to enable the interaction with partner transcription factors. Some post-translational modifications known to regulate the functional state of transcription factors are phosphorylation, acetylation, SUMOylation and ubiquitylation.

Transcription factors can be divided in two main categories: activators and repressors. While activators can interact directly or indirectly with the core machinery of transcription through enhancer binding, repressors predominantly recruit co-repressor complexes leading to transcriptional repression by chromatin condensation of enhancer regions. It may also happen that a repressor may function by allosteric competition against a determined activator to repress gene expression: overlapping DNA-binding motifs for both activators and repressors induce a physical competition to occupy the site of binding. If the repressor has a higher affinity for its motif than the activator, transcription would be effectively blocked in the presence of the repressor.

Tight regulatory control is achieved by the highly dynamic nature of transcription factors. Again, many different mechanisms exist to control whether a transcription factor is active. These mechanisms include control over protein localization or control over whether the protein can bind DNA.{{cite journal | vauthors = Whiteside ST, Goodbourn S | title = Signal transduction and nuclear targeting: regulation of transcription factor activity by subcellular localisation | journal = J. Cell Sci. | volume = 104 ( Pt 4) | pages = 949–55 | date = April 1993 | issue = 4 | doi = 10.1242/jcs.104.4.949 | pmid = 8314906 }} An example of this is the protein HSF1, which remains bound to Hsp70 in the cytosol and is only translocated into the nucleus upon cellular stress such as heat shock. Thus the genes under the control of this transcription factor will remain untranscribed unless the cell is subjected to stress.{{cite journal | vauthors = Vihervaara A, Sistonen L | title = HSF1 at a glance | journal = J. Cell Sci. | volume = 127 | issue = Pt 2 | pages = 261–6 | date = January 2014 | pmid = 24421309 | doi = 10.1242/jcs.132605 | doi-access = free }}

Enhancers or cis-regulatory modules/elements (CRM/CRE) are non-coding DNA sequences containing multiple activator and repressor binding sites. Enhancers range from 200 bp to 1 kb in length and can be either proximal, 5’ upstream to the promoter or within the first intron of the regulated gene, or distal, in introns of neighboring genes or intergenic regions far away from the locus. Through DNA looping, active enhancers contact the promoter dependently of the core DNA binding motif promoter specificity.{{cite journal | vauthors = Levine M | title = Transcriptional enhancers in animal development and evolution | journal = Curr. Biol. | volume = 20 | issue = 17 | pages = R754–63 | date = September 2010 | pmid = 20833320 | pmc = 4280268 | doi = 10.1016/j.cub.2010.06.070 | bibcode = 2010CBio...20.R754L }} Promoter-enhancer dichotomy provides the basis for the functional interaction between transcription factors and transcriptional core machinery to trigger RNA Pol II escape from the promoter. Whereas one could think that there is a 1:1 enhancer-promoter ratio, studies of the human genome predict that an active promoter interacts with 4 to 5 enhancers. Similarly, enhancers can regulate more than one gene without linkage restriction and are said to “skip” neighboring genes to regulate more distant ones. Even though infrequent, transcriptional regulation can involve elements located in a chromosome different from one where the promoter resides. Proximal enhancers or promoters of neighboring genes can serve as platforms to recruit more distal elements.{{cite journal | vauthors = van Arensbergen J, van Steensel B, Bussemaker HJ | title = In search of the determinants of enhancer-promoter interaction specificity | journal = Trends Cell Biol. | volume = 24 | issue = 11 | pages = 695–702 | date = November 2014 | pmid = 25160912 | pmc = 4252644 | doi = 10.1016/j.tcb.2014.07.004 }}

{{cleanup section|reason=Duplication with Enhancer (genetics). Maybe {{tlx|main}} will do??|date=September 2021}}

File:Regulation of transcription in mammals.jpg DNA regulatory sequence of its target gene by formation of a chromosome loop. This can initiate messenger RNA (mRNA) synthesis by RNA polymerase II (RNAP II) bound to the promoter at the transcription start site of the gene. The loop is stabilized by one architectural protein anchored to the enhancer and one anchored to the promoter and these proteins are joined to form a dimer (red zigzags). Specific regulatory transcription factors bind to DNA sequence motifs on the enhancer. General transcription factors bind to the promoter. When a transcription factor is activated by a signal (here indicated as phosphorylation shown by a small red star on a transcription factor on the enhancer) the enhancer is activated and can now activate its target promoter. The active enhancer is transcribed on each strand of DNA in opposite directions by bound RNAP IIs. Mediator (a complex consisting of about 26 proteins in an interacting structure) communicates regulatory signals from the enhancer DNA-bound transcription factors to the promoter.]]

Up-regulated expression of genes in mammals can be initiated when signals are transmitted to the promoters associated with the genes. Cis-regulatory DNA sequences that are located in DNA regions distant from the promoters of genes can have very large effects on gene expression, with some genes undergoing up to 100-fold increased expression due to such a cis-regulatory sequence.{{cite journal | vauthors = Beagan JA, Pastuzyn ED, Fernandez LR, Guo MH, Feng K, Titus KR, Chandrashekar H, Shepherd JD, Phillips-Cremins JE | display-authors = 6 | title = Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression | journal = Nature Neuroscience | volume = 23 | issue = 6 | pages = 707–717 | date = June 2020 | pmid = 32451484 | pmc = 7558717 | doi = 10.1038/s41593-020-0634-6 }} These cis-regulatory sequences include enhancers, silencers, insulators and tethering elements.{{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 = Frontiers in Cell and Developmental Biology | volume = 8 | issue = | pages = 592164 | date = 2020 | pmid = 33102493 | pmc = 7554316 | doi = 10.3389/fcell.2020.592164 | doi-access = free }} Among this constellation of sequences, enhancers and their associated transcription factor proteins have a leading role in the regulation of gene expression.{{cite journal | vauthors = Spitz F, Furlong EE | title = Transcription factors: from enhancer binding to developmental control | journal = Nature Reviews. Genetics | volume = 13 | issue = 9 | pages = 613–26 | date = September 2012 | pmid = 22868264 | doi = 10.1038/nrg3207 | s2cid = 205485256 }}

Enhancers are sequences of the genome that are major gene-regulatory elements. Enhancers control cell-type-specific gene expression programs, most often by looping through long distances to come in physical proximity with the promoters of their target genes.{{cite journal | vauthors = Schoenfelder S, Fraser P | title = Long-range enhancer-promoter contacts in gene expression control | journal = Nature Reviews. Genetics | volume = 20 | issue = 8 | pages = 437–455 | date = August 2019 | pmid = 31086298 | doi = 10.1038/s41576-019-0128-0 | s2cid = 152283312 }} In a study of brain cortical neurons, 24,937 loops were found, bringing enhancers to promoters. Multiple enhancers, each often at tens or hundred of thousands of nucleotides distant from their target genes, loop to their target gene promoters and coordinate with each other to control expression of their common target gene.

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).{{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 | display-authors = 6 | title = YY1 Is a Structural Regulator of Enhancer-Promoter Loops | journal = Cell | volume = 171 | issue = 7 | pages = 1573–1588.e28 | date = December 2017 | pmid = 29224777 | pmc = 5785279 | doi = 10.1016/j.cell.2017.11.008 }} Several cell function specific transcription factor proteins (in 2018 Lambert et al. indicated there were about 1,600 transcription factors in a human cell{{cite journal | vauthors = Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen X, Taipale J, Hughes TR, Weirauch MT | display-authors = 6 | 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 | doi-access = free }}) generally bind to specific motifs on an enhancer{{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 = Proceedings of the National Academy of Sciences of the United States of America | volume = 115 | issue = 30 | pages = E7222–E7230 | date = July 2018 | pmid = 29987030 | pmc = 6065035 | doi = 10.1073/pnas.1804663115 | bibcode = 2018PNAS..115E7222G | doi-access = free }} and a small combination of these enhancer-bound transcription factors, when brought close to a promoter by a DNA loop, govern the level of transcription of the target gene. Mediator (coactivator) (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 (RNAP II) enzyme bound to the promoter.{{cite journal | vauthors = Allen BL, Taatjes DJ | title = The Mediator complex: a central integrator of transcription | journal = Nature Reviews. Molecular Cell Biology | volume = 16 | issue = 3 | pages = 155–66 | date = March 2015 | pmid = 25693131 | pmc = 4963239 | doi = 10.1038/nrm3951 }}

Enhancers, when active, are generally transcribed from both strands of DNA with RNA polymerases acting in two different directions, producing two eRNAs as illustrated in the Figure.{{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 & Development | volume = 32 | issue = 1 | pages = 42–57 | date = January 2018 | pmid = 29378788 | pmc = 5828394 | doi = 10.1101/gad.308619.117 }} 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 a transcription factor bound to an enhancer in the illustration).{{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 = The EMBO Journal | volume = 22 | issue = 2 | pages = 281–91 | date = January 2003 | pmid = 12514134 | pmc = 140103 | doi = 10.1093/emboj/cdg028 }} An activated enhancer begins transcription of its RNA before activating a promoter to initiate transcription of messenger RNA from its target gene.{{cite journal | vauthors = Carullo NV, Phillips Iii RA, Simon RC, Soto SA, Hinds JE, Salisbury AJ, Revanna JS, Bunner KD, Ianov L, Sultan FA, Savell KE, Gersbach CA, Day JJ | display-authors = 6 | title = Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems | journal = Nucleic Acids Research | volume = 48 | issue = 17 | pages = 9550–9570 | date = September 2020 | pmid = 32810208 | pmc = 7515708 | doi = 10.1093/nar/gkaa671 }}

{{clear}}

Typical enhancers are often of the size 151–240 base pairs.{{cite journal |vauthors=Meuleman W, Muratov A, Rynes E, Halow J, Lee K, Bates D, Diegel M, Dunn D, Neri F, Teodosiadis A, Reynolds A, Haugen E, Nelson J, Johnson A, Frerker M, Buckley M, Sandstrom R, Vierstra J, Kaul R, Stamatoyannopoulos J |title=Index and biological spectrum of human DNase I hypersensitive sites |journal=Nature |volume=584 |issue=7820 |pages=244–251 |date=August 2020 |pmid=32728217 |pmc=7422677 |doi=10.1038/s41586-020-2559-3 |url=}}

{{main|Super-enhancer}}

While enhancers are needed for transcription of a gene above a low level, clusters of enhancers, known as super-enhancers, can cause transcription of a target gene at a very high level.

File:Super-enhancer.jpg

Super-enhancers are a group of typical enhancers, all located within a region of 10,000 to 60,000 nucleotides.{{cite journal |vauthors=Wang X, Cairns MJ, Yan J |title=Super-enhancers in transcriptional regulation and genome organization |journal=Nucleic Acids Res |volume=47 |issue=22 |pages=11481–11496 |date=December 2019 |pmid=31724731 |pmc=7145697 |doi=10.1093/nar/gkz1038 |url=}}{{cite journal |vauthors=Kang Y, Kang J, Kim A |title=Histone H3K4me1 strongly activates the DNase I hypersensitive sites in super-enhancers than those in typical enhancers |journal=Biosci Rep |volume=41 |issue=7 |pages= |date=July 2021 |pmid=34195788 |pmc=8264496 |doi=10.1042/BSR20210691 |url=}} The typical enhancers within a super-enhancer simultaneously loop over from a distance to strongly increase initiation and transcription of a gene. The illustration in this section shows a super-enhancer of about 12,000 base pairs in length with four typical enhancers within its length. The enhancers are each associated with the same gene, transmitting signals from the transcription factors on each enhancer through a mediator protein complex to the promoter of the gene. Each typical enhancer within the cluster interacts with its own mediator multi-protein complex. The protein BRD4 complexes with each typical enhancer and stabilizes the super-enhancer structure.{{cite journal |vauthors=Hamdan FH, Johnsen SA |title=Super enhancers - new analyses and perspectives on the low hanging fruit |journal=Transcription |volume=9 |issue=2 |pages=123–130 |date=2018 |pmid=28980882 |pmc=5834217 |doi=10.1080/21541264.2017.1372044 |url=}} Thus, there are a large number of proteins present in close association on a super-enhancer, including BRD4 proteins, transcription factors, 26 mediator proteins for each enhancer, etc.). Most of these proteins have a structured domain as well as a tail with an intrinsically disordered region.{{cite journal |vauthors=Boija A, Klein IA, Sabari BR, Dall'Agnese A, Coffey EL, Zamudio AV, Li CH, Shrinivas K, Manteiga JC, Hannett NM, Abraham BJ, Afeyan LK, Guo YE, Rimel JK, Fant CB, Schuijers J, Lee TI, Taatjes DJ, Young RA |title=Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains |journal=Cell |volume=175 |issue=7 |pages=1842–1855.e16 |date=December 2018 |pmid=30449618 |pmc=6295254 |doi=10.1016/j.cell.2018.10.042 |url=}} The intrinsically disordered regions of these proteins interact with each other and usually form a water-excluding gel (phase-separated condensate) around the super-enhancer.

As examples, in the case of the mouse α-globin super-enhancer, the five typical enhancers within the super-enhancer, acting together, increase transcription of the α-globin gene by 450-fold.{{cite journal |vauthors=Blayney JW, Francis H, Rampasekova A, Camellato B, Mitchell L, Stolper R, Cornell L, Babbs C, Boeke JD, Higgs DR, Kassouf M |title=Super-enhancers include classical enhancers and facilitators to fully activate gene expression |journal=Cell |volume=186 |issue=26 |pages=5826–5839.e18 |date=December 2023 |pmid=38101409 |pmc=10858684 |doi=10.1016/j.cell.2023.11.030 |url=}} In the case of the mouse Wap super-enhancer, the three typical enhancers, acting together, increase transcription of the Wap gene by 1000-fold.{{cite journal |vauthors=Shin HY, Willi M, HyunYoo K, Zeng X, Wang C, Metser G, Hennighausen L |title=Hierarchy within the mammary STAT5-driven Wap super-enhancer |journal=Nat Genet |volume=48 |issue=8 |pages=904–911 |date=August 2016 |pmid=27376239 |pmc=4963296 |doi=10.1038/ng.3606 |url=}}

In many types of cells, there are usually thousands of active typical enhancers and a few hundred super-enhancers. Super-enhancers (SEs) usually drive 2% to 4% of the actively transcribed regions of the genome. For instance, immune-system non-stimulated B cells have 140 super-enhancers (SEs) and 4,290 typical enhancers (TEs) (3.2% SEs).{{cite journal |vauthors=Michida H, Imoto H, Shinohara H, Yumoto N, Seki M, Umeda M, Hayashi T, Nikaido I, Kasukawa T, Suzuki Y, Okada-Hatakeyama M |title=The Number of Transcription Factors at an Enhancer Determines Switch-like Gene Expression |journal=Cell Rep |volume=31 |issue=9 |pages=107724 |date=June 2020 |pmid=32492432 |doi=10.1016/j.celrep.2020.107724 |url=|doi-access=free }} Similarly, in mouse embryonic stem cells, there are 231 SEs compared to 8,794 TEs (2.6% SEs).{{cite journal |vauthors=Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, Rahl PB, Lee TI, Young RA |title=Master transcription factors and mediator establish super-enhancers at key cell identity genes |journal=Cell |volume=153 |issue=2 |pages=307–19 |date=April 2013 |pmid=23582322 |pmc=3653129 |doi=10.1016/j.cell.2013.03.035 |url=}} In neural stem cells there are 445 SEs and 9,436 TEs (4.7% SEs).{{cite journal |vauthors=Quevedo M, Meert L, Dekker MR, Dekkers DH, Brandsma JH, van den Berg DL, Ozgür Z, van IJcken WF, Demmers J, Fornerod M, Poot RA |title=Mediator complex interaction partners organize the transcriptional network that defines neural stem cells |journal=Nat Commun |volume=10 |issue=1 |pages=2669 |date=June 2019 |pmid=31209209 |pmc=6573065 |doi=10.1038/s41467-019-10502-8 |bibcode=2019NatCo..10.2669Q |url=}}

While super-enhancers are only active at 2-4% of actively transcribed sites in a cell, they strongly recruit transcription machinery. The super-enhancers in a cell generally utilize 12% to 36% of the RNA polymerases, mediator proteins, BRD4 proteins, and other transcription machinery of the cell.{{cite journal |vauthors=Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, Hoke HA, Young RA |title=Super-enhancers in the control of cell identity and disease |journal=Cell |volume=155 |issue=4 |pages=934–47 |date=November 2013 |pmid=24119843 |pmc=3841062 |doi=10.1016/j.cell.2013.09.053 |url=}}

Transcriptional initiation, termination and regulation are mediated by “DNA looping” which brings together promoters, enhancers, transcription factors and RNA processing factors to accurately regulate gene expression.{{cite journal | vauthors = Mercer TR, Mattick JS | title = Understanding the regulatory and transcriptional complexity of the genome through structure | journal = Genome Res. | volume = 23 | issue = 7 | pages = 1081–8 | date = July 2013 | pmid = 23817049 | pmc = 3698501 | doi = 10.1101/gr.156612.113 }} Chromosome conformation capture (3C) and more recently Hi-C techniques provided evidence that active chromatin regions are “compacted” in nuclear domains or bodies where transcriptional regulation is enhanced.{{cite journal | vauthors = Dekker J, Marti-Renom MA, Mirny LA | title = Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data | journal = Nat. Rev. Genet. | volume = 14 | issue = 6 | pages = 390–403 | date = June 2013 | pmid = 23657480 | pmc = 3874835 | doi = 10.1038/nrg3454 }} The configuration of the genome is essential for enhancer-promoter proximity. Cell-fate decisions are mediated upon highly dynamic genomic reorganizations at interphase to modularly switch on or off entire gene regulatory networks through short to long range chromatin rearrangements.{{cite journal | vauthors = Gómez-Díaz E, Corces VG | title = Architectural proteins: regulators of 3D genome organization in cell fate | journal = Trends Cell Biol. | volume = 24 | issue = 11 | pages = 703–11 | date = November 2014 | pmid = 25218583 | pmc = 4254322 | doi = 10.1016/j.tcb.2014.08.003 }} Related studies demonstrate that metazoan genomes are partitioned in structural and functional units around a megabase long called Topological association domains (TADs) containing dozens of genes regulated by hundreds of enhancers distributed within large genomic regions containing only non-coding sequences. The function of TADs is to regroup enhancers and promoters interacting together within a single large functional domain instead of having them spread in different TADs.{{cite journal | vauthors = Smallwood A, Ren B | title = Genome organization and long-range regulation of gene expression by enhancers | journal = Curr. Opin. Cell Biol. | volume = 25 | issue = 3 | pages = 387–94 | date = June 2013 | pmid = 23465541 | pmc = 4180870 | doi = 10.1016/j.ceb.2013.02.005 }} However, studies of mouse development point out that two adjacent TADs may regulate the same gene cluster. The most relevant study on limb evolution shows that the TAD at the 5’ of the HoxD gene cluster in tetrapod genomes drives its expression in the distal limb bud embryos, giving rise to the hand, while the one located at 3’ side does it in the proximal limb bud, giving rise to the arm.{{cite journal | vauthors = Woltering JM, Noordermeer D, Leleu M, Duboule D | title = Conservation and divergence of regulatory strategies at Hox Loci and the origin of tetrapod digits | journal = PLOS Biol. | volume = 12 | issue = 1 | pages = e1001773 | date = January 2014 | pmid = 24465181 | pmc = 3897358 | doi = 10.1371/journal.pbio.1001773 | doi-access = free }} Still, it is not known whether TADs are an adaptive strategy to enhance regulatory interactions or an effect of the constrains on these same interactions.

TAD boundaries are often composed by housekeeping genes, tRNAs, other highly expressed sequences and Short Interspersed Elements (SINE). While these genes may take advantage of their border position to be ubiquitously expressed, they are not directly linked with TAD edge formation. The specific molecules identified at boundaries of TADs are called insulators or architectural proteins because they not only block enhancer leaky expression but also ensure an accurate compartmentalization of cis-regulatory inputs to the targeted promoter. These insulators are DNA-binding proteins like CTCF and TFIIIC that help recruiting structural partners such as cohesins and condensins. The localization and binding of architectural proteins to their corresponding binding sites is regulated by post-translational modifications.{{cite journal | vauthors = Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R, Thurman RE, Kaul R, Myers RM, Stamatoyannopoulos JA |author-link14=John Stamatoyannopoulos | title = Widespread plasticity in CTCF occupancy linked to DNA methylation | journal = Genome Res. | volume = 22 | issue = 9 | pages = 1680–8 | date = September 2012 | pmid = 22955980 | pmc = 3431485 | doi = 10.1101/gr.136101.111 }} DNA binding motifs recognized by architectural proteins are either of high occupancy and at around a megabase of each other or of low occupancy and inside TADs. High occupancy sites are usually conserved and static while intra-TADs sites are dynamic according to the state of the cell therefore TADs themselves are compartmentalized in subdomains that can be called subTADs from few kb up to a TAD long (19). When architectural binding sites are at less than 100 kb from each other, Mediator proteins are the architectural proteins cooperate with cohesin. For subTADs larger than 100 kb and TAD boundaries, CTCF is the typical insulator found to interact with cohesion.{{cite journal | vauthors = Phillips-Cremins JE, Sauria ME, Sanyal A, Gerasimova TI, Lajoie BR, Bell JS, Ong CT, Hookway TA, Guo C, Sun Y, Bland MJ, Wagstaff W, Dalton S, McDevitt TC, Sen R, Dekker J, Taylor J, Corces VG|display-authors = 6 | title = Architectural protein subclasses shape 3D organization of genomes during lineage commitment | journal = Cell | volume = 153 | issue = 6 | pages = 1281–95 | date = June 2013 | pmid = 23706625 | pmc = 3712340 | doi = 10.1016/j.cell.2013.04.053 }}

In eukaryotes, ribosomal rRNA and the tRNAs involved in translation are controlled by RNA polymerase I (Pol I) and RNA polymerase III (Pol III) . RNA Polymerase II (Pol II) is responsible for the production of messenger RNA (mRNA) within the cell. Particularly for Pol II, much of the regulatory checkpoints in the transcription process occur in the assembly and escape of the pre-initiation complex. A gene-specific combination of transcription factors will recruit TFIID and/or TFIIA to the core promoter, followed by the association of TFIIB, creating a stable complex onto which the rest of the General Transcription Factors (GTFs) can assemble.{{cite journal | vauthors = Thomas MC, Chiang CM | title = The general transcription machinery and general cofactors | journal = Crit. Rev. Biochem. Mol. Biol. | volume = 41 | issue = 3 | pages = 105–78 | date = 2006 | pmid = 16858867 | doi = 10.1080/10409230600648736 | citeseerx = 10.1.1.376.5724 | s2cid = 13073440 }} This complex is relatively stable, and can undergo multiple rounds of transcription initiation.{{cite book|last1=Voet|first1=Donald Voet, Judith G.|title=Biochemistry|date=2011|publisher=John Wiley & Sons|location=Hoboken, NJ|isbn=978-0470917459|edition=4th}}

After the binding of TFIIB and TFIID, Pol II the rest of the GTFs can assemble. This assembly is marked by the post-translational modification (typically phosphorylation) of the C-terminal domain (CTD) of Pol II through a number of kinases.{{cite journal | vauthors = Napolitano G, Lania L, Majello B | title = RNA polymerase II CTD modifications: how many tales from a single tail | journal = J. Cell. Physiol. | volume = 229 | issue = 5 | pages = 538–44 | date = May 2014 | pmid = 24122273 | doi = 10.1002/jcp.24483 | s2cid = 44613555 }} The CTD is a large, unstructured domain extending from the RbpI subunit of Pol II, and consists of many repeats of the heptad sequence YSPTSPS. TFIIH, the helicase that remains associated with Pol II throughout transcription, also contains a subunit with kinase activity which will phosphorylate the serines 5 in the heptad sequence. Similarly, both CDK8 (a subunit of the massive multiprotein Mediator complex) and CDK9 (a subunit of the p-TEFb elongation factor), have kinase activity towards other residues on the CTD.{{cite journal | vauthors = Chapman RD, Conrad M, Eick D | title = Role of the mammalian RNA polymerase II C-terminal domain (CTD) nonconsensus repeats in CTD stability and cell proliferation | journal = Mol. Cell. Biol. | volume = 25 | issue = 17 | pages = 7665–74 | date = September 2005 | pmid = 16107713 | pmc = 1190292 | doi = 10.1128/MCB.25.17.7665-7674.2005 }} These phosphorylation events promote the transcription process and serve as sites of recruitment for mRNA processing machinery. All three of these kinases respond to upstream signals, and failure to phosphorylate the CTD can lead to a stalled polymerase at the promoter.

{{main|Regulation of transcription in cancer}}

In vertebrates, the majority of gene promoters contain a CpG island with numerous CpG sites.{{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=Proc. Natl. Acad. Sci. U.S.A. |volume=103 |issue=5 |pages=1412–7 |year=2006 |pmid=16432200 |pmc=1345710 |doi=10.1073/pnas.0510310103 |bibcode=2006PNAS..103.1412S |doi-access=free }} When many of a gene's promoter CpG sites are methylated the gene becomes silenced.{{cite journal |vauthors=Bird A |title=DNA methylation patterns and epigenetic memory |journal=Genes Dev. |volume=16 |issue=1 |pages=6–21 |year=2002 |pmid=11782440 |doi=10.1101/gad.947102 |doi-access=free }} Colorectal cancers typically have 3 to 6 driver mutations and 33 to 66 hitchhiker or passenger mutations.{{cite journal |vauthors=Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA, Kinzler KW |title=Cancer genome landscapes |journal=Science |volume=339 |issue=6127 |pages=1546–58 |year=2013 |pmid=23539594 |pmc=3749880 |doi=10.1126/science.1235122 |bibcode=2013Sci...339.1546V }} However, transcriptional silencing may be of more importance than mutation in causing progression to cancer. For example, in colorectal cancers about 600 to 800 genes are transcriptionally silenced by CpG island methylation (see regulation of transcription in cancer). Transcriptional repression in cancer can also occur by other epigenetic mechanisms, such as altered expression of microRNAs.{{cite journal |vauthors=Tessitore A, Cicciarelli G, Del Vecchio F, Gaggiano A, Verzella D, Fischietti M, Vecchiotti D, Capece D, Zazzeroni F, Alesse E |title=MicroRNAs in the DNA Damage/Repair Network and Cancer |journal=Int J Genom |volume=2014 |pages=1–10 |year=2014 |pmid=24616890 |pmc=3926391 |doi=10.1155/2014/820248 |doi-access=free }} In breast cancer, transcriptional repression of BRCA1 may occur more frequently by over-expressed microRNA-182 than by hypermethylation of the BRCA1 promoter (see Low expression of BRCA1 in breast and ovarian cancers).

{{reflist|30em}}

• [http://plantregmap.cbi.pku.edu.cn/ Plant Transcription Factor Database and Plant Transcriptional Regulation Data and Analysis Platform]
• [https://news.mit.edu/2018/mit-whitehead-institute-researchers-activating-new-understanding-gene-regulation-1116 MIT : Activating a new understanding of gene regulation]

{{gene expression}}

Category:Gene expression