Editing Promoter (genetics) (section)

=== Eukaryotic ===
Gene promoters are typically located upstream of the gene and can have regulatory elements several kilobases away from the transcriptional start site (enhancers). In eukaryotes, the transcriptional complex can cause the DNA to bend back on itself, which allows for placement of regulatory sequences far from the actual site of transcription. Eukaryotic RNA-polymerase-II-dependent promoters can contain a [[TATA box]] ([[consensus sequence]] TATAAA), which is recognized by the [[general transcription factor]] [[TATA-binding protein]] (TBP); and a [[B recognition element]] (BRE), which is recognized by the general transcription factor [[TFIIB]].<ref name="Smale2003" /><ref>{{cite journal | vauthors = Gershenzon NI, Ioshikhes IP | title = Synergy of human Pol II core promoter elements revealed by statistical sequence analysis | journal = Bioinformatics | volume = 21 | issue = 8 | pages = 1295–1300 | date = April 2005 | pmid = 15572469 | doi = 10.1093/bioinformatics/bti172 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Lagrange T, Kapanidis AN, Tang H, Reinberg D, Ebright RH | title = New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB | journal = Genes & Development | volume = 12 | issue = 1 | pages = 34–44 | date = January 1998 | pmid = 9420329 | pmc = 316406 | doi = 10.1101/gad.12.1.34 }}</ref> The TATA element and BRE typically are located close to the transcriptional start site (typically within 30 to 40 base pairs).

Eukaryotic promoter regulatory sequences typically bind proteins called transcription factors that are involved in the formation of the transcriptional complex. An example is the [[E-box]] (sequence CACGTG), which binds transcription factors in the [[basic helix-loop-helix]] (bHLH) family (e.g. [[BMAL1-Clock]], [[cMyc]]).<ref>{{cite journal | vauthors = Levine M, Tjian R | title = Transcription regulation and animal diversity | journal = Nature | volume = 424 | issue = 6945 | pages = 147–151 | date = July 2003 | pmid = 12853946 | doi = 10.1038/nature01763 | s2cid = 4373712 | bibcode = 2003Natur.424..147L }}</ref> Some promoters that are targeted by multiple transcription factors might achieve a hyperactive state, leading to increased transcriptional activity.<ref name=Liefke2015>{{cite journal | vauthors = Liefke R, Windhof-Jaidhauser IM, Gaedcke J, Salinas-Riester G, Wu F, Ghadimi M, Dango S | title = The oxidative demethylase ALKBH3 marks hyperactive gene promoters in human cancer cells | journal = Genome Medicine | volume = 7 | issue = 1 | pages = 66 | date = June 2015 | pmid = 26221185 | pmc = 4517488 | doi = 10.1186/s13073-015-0180-0 | doi-access = free }}</ref>
* Core promoter – the minimal portion of the promoter required to properly initiate transcription<ref name="Smale2003" >{{cite journal | vauthors = Smale ST, Kadonaga JT | title = The RNA polymerase II core promoter | journal = Annual Review of Biochemistry | volume = 72 | pages = 449–479 | year = 2003 | pmid = 12651739 | doi = 10.1146/annurev.biochem.72.121801.161520 }}</ref>
** Includes the transcription start site (TSS) and elements directly upstream
** A binding site for RNA polymerase
*** [[RNA polymerase I]]: transcribes genes encoding 18S, 5.8S and 28S [[ribosomal RNA]]s
*** [[RNA polymerase II]]: transcribes genes encoding [[messenger RNA]] and certain [[small nuclear RNA]]s and [[microRNA]]
*** [[RNA polymerase III]]: transcribes genes encoding [[transfer RNA]], [[5S ribosomal RNA|5s ribosomal RNAs]] and other small RNAs
** General transcription factor binding sites, e.g. [[TATA box]], [[B recognition element]].
** Many other elements/motifs may be present. There is no such thing as a set of "universal elements" found in every core promoter.<ref name="pmid19682982">{{cite journal | vauthors = Juven-Gershon T, Kadonaga JT | title = Regulation of gene expression via the core promoter and the basal transcriptional machinery | journal = Developmental Biology | volume = 339 | issue = 2 | pages = 225–229 | date = March 2010 | pmid = 19682982 | pmc = 2830304 | doi = 10.1016/j.ydbio.2009.08.009 }}</ref>
* Proximal promoter – the proximal sequence upstream of the gene that tends to contain primary regulatory elements
** Approximately 250 base pairs upstream of the start site
** Specific [[transcription factor binding site]]s
* [[Distal promoter]] – the distal sequence upstream of the gene that may contain additional regulatory elements, often with a weaker influence than the proximal promoter
** Anything further upstream (but not an enhancer or other regulatory region whose influence is positional/orientation independent)
** Specific transcription factor binding sites

====Mammalian promoters====
{{cleanup section|reason=Text about mammals highly duplicated among uses of the same picture -- can we make a "canonical" version and redirect people there?|date=September 2021}}
[[File:Regulation of transcription in mammals.jpg|thumb|left|500px| '''Regulation of transcription in mammals'''. An active [[Enhancer (genetics)|enhancer]] regulatory region is enabled to interact with the promoter region 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 (biology)|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 factor]]s bind to DNA sequence motifs on the enhancer. [[General transcription factor]]s 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 (coactivator)]] (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 is initiated when signals are transmitted to the promoters associated with the genes. Promoter DNA sequences may include different elements such as [[CpG site|CpG islands]] (present in about 70% of promoters), a [[TATA box]] (present in about 24% of promoters), [[Initiator element|initiator (Inr)]] (present in about 49% of promoters), upstream and downstream TFIIB recognition elements (BREu and BREd) (present in about 22% of promoters), and downstream core promoter element (DPE) (present in about 12% of promoters).<ref name=Yang>{{cite journal | vauthors = Yang C, Bolotin E, Jiang T, Sladek FM, Martinez E | title = Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters | journal = Gene | volume = 389 | issue = 1 | pages = 52–65 | date = March 2007 | pmid = 17123746 | pmc = 1955227 | doi = 10.1016/j.gene.2006.09.029 }}</ref> The presence of multiple [[DNA methylation|methylated CpG sites]] in CpG islands of promoters causes stable silencing of genes.<ref name=Bird>{{cite journal | vauthors = Bird A | title = DNA methylation patterns and epigenetic memory | journal = Genes & Development | volume = 16 | issue = 1 | pages = 6–21 | date = January 2002 | pmid = 11782440 | doi = 10.1101/gad.947102 | doi-access = free }}</ref> However, the presence or absence of the other elements have relatively small effects on gene expression in experiments.<ref name=Weingarten-Gabbay>{{cite journal | vauthors = Weingarten-Gabbay S, Nir R, Lubliner S, Sharon E, Kalma Y, Weinberger A, Segal E | title = Systematic interrogation of human promoters | journal = Genome Research | volume = 29 | issue = 2 | pages = 171–183 | date = February 2019 | pmid = 30622120 | pmc = 6360817 | doi = 10.1101/gr.236075.118 }}</ref> Two sequences, the TATA box and Inr, caused small but significant increases in expression (45% and 28% increases, respectively). The BREu and the BREd elements significantly decreased expression by 35% and 20%, respectively, and the DPE element had no detected effect on expression.<ref name=Weingarten-Gabbay />

[[Cis-regulatory element|Cis-regulatory modules]] that are localized 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 module.<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 | 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 }}</ref> These cis-regulatory modules 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 = 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 }}</ref> Among this constellation of elements, enhancers and their associated [[transcription factors]] have a leading role in the regulation of gene expression.<ref name="pmid22868264">{{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 = 613–626 | date = September 2012 | pmid = 22868264 | doi = 10.1038/nrg3207 | s2cid = 205485256 }}</ref>

[[Enhancer (genetics)|Enhancers]] are regions 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.<ref name=Schoenfelder>{{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 }}</ref>  In a study of brain cortical neurons, 24,937 loops were found, bringing enhancers to 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 coordinate with each other to control expression 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 | 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 }}</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 | 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 }}</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 = 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 }}</ref> 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 (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 = Nature Reviews. Molecular Cell Biology | volume = 16 | issue = 3 | pages = 155–166 | date = March 2015 | pmid = 25693131 | pmc = 4963239 | doi = 10.1038/nrm3951 }}</ref>

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.<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 & Development | volume = 32 | issue = 1 | pages = 42–57 | date = January 2018 | pmid = 29378788 | pmc = 5828394 | doi = 10.1101/gad.308619.117 }}</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 = The EMBO Journal | volume = 22 | issue = 2 | pages = 281–291 | date = January 2003 | pmid = 12514134 | pmc = 140103 | doi = 10.1093/emboj/cdg028 }}</ref>  An activated enhancer begins transcription of its RNA before activating a promoter to initiate transcription of messenger RNA from its target gene.<ref name="pmid32810208">{{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 }}</ref>

====Bidirectional (mammalian)====
Bidirectional promoters are short (<1 kbp) intergenic regions of [[DNA]] between the 5' ends of the [[genes]] in a bidirectional gene pair.<ref name="Trinklein">{{cite journal | vauthors = Trinklein ND, Aldred SF, Hartman SJ, Schroeder DI, Otillar RP, Myers RM | title = An abundance of bidirectional promoters in the human genome | journal = Genome Research | volume = 14 | issue = 1 | pages = 62–66 | date = January 2004 | pmid = 14707170 | pmc = 314279 | doi = 10.1101/gr.1982804 }}</ref> A "bidirectional gene pair" refers to two adjacent genes coded on opposite strands, with their 5' ends oriented toward one another.<ref>{{cite journal | vauthors = Yang MQ, Koehly LM, Elnitski LL | title = Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes | journal = PLOS Computational Biology | volume = 3 | issue = 4 | pages = e72 | date = April 2007 | pmid = 17447839 | pmc = 1853124 | doi = 10.1371/journal.pcbi.0030072 | bibcode = 2007PLSCB...3...72Y | doi-access = free }}</ref> The two genes are often functionally related, and modification of their shared promoter region allows them to be co-regulated and thus co-expressed.<ref>{{cite journal | vauthors = Adachi N, Lieber MR | title = Bidirectional gene organization: a common architectural feature of the human genome | journal = Cell | volume = 109 | issue = 7 | pages = 807–809 | date = June 2002 | pmid = 12110178 | doi = 10.1016/S0092-8674(02)00758-4 | s2cid = 8556921 | doi-access = free }}</ref> Bidirectional promoters are a common feature of [[mammal]]ian [[genome]]s.<ref>{{cite journal | vauthors = Koyanagi KO, Hagiwara M, Itoh T, Gojobori T, Imanishi T | title = Comparative genomics of bidirectional gene pairs and its implications for the evolution of a transcriptional regulation system | journal = Gene | volume = 353 | issue = 2 | pages = 169–176 | date = July 2005 | pmid = 15944140 | doi = 10.1016/j.gene.2005.04.027 }}</ref> About 11% of human genes are bidirectionally paired.<ref name="Trinklein" />

Bidirectionally paired genes in the [[Gene Ontology]] database shared at least one database-assigned functional category with their partners 47% of the time.<ref>{{cite journal | vauthors = Liu B, Chen J, Shen B | title = Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs | journal = BMC Systems Biology | volume = 5 | issue = Suppl 1 | pages = S2 | date = May 2011 | pmid = 21689477 | pmc = 3121118 | doi = 10.1186/1752-0509-5-S1-S2 | doi-access = free }}</ref> [[Microarray]] analysis has shown bidirectionally paired genes to be co-expressed to a higher degree than random genes or neighboring unidirectional genes.<ref name="Trinklein" /> Although co-expression does not necessarily indicate co-regulation, [[methylation]] of bidirectional promoter regions has been shown to downregulate both genes, and demethylation to upregulate both genes.<ref name="Shu">{{cite journal | vauthors = Shu J, Jelinek J, Chang H, Shen L, Qin T, Chung W, Oki Y, Issa JP | display-authors = 6 | title = Silencing of bidirectional promoters by DNA methylation in tumorigenesis | journal = Cancer Research | volume = 66 | issue = 10 | pages = 5077–5084 | date = May 2006 | pmid = 16707430 | doi = 10.1158/0008-5472.CAN-05-2629 | doi-access = free }}</ref> There are exceptions to this, however. In some cases (about 11%), only one gene of a bidirectional pair is expressed.<ref name="Trinklein" /> In these cases, the promoter is implicated in suppression of the non-expressed gene. The mechanism behind this could be competition for the same polymerases, or [[chromatin]] modification. Divergent transcription could shift [[nucleosomes]] to upregulate transcription of one gene, or remove bound transcription factors to downregulate transcription of one gene.<ref name="dx">{{cite journal | vauthors = Wei W, Pelechano V, Järvelin AI, Steinmetz LM | title = Functional consequences of bidirectional promoters | journal = Trends in Genetics | volume = 27 | issue = 7 | pages = 267–276 | date = July 2011 | pmid = 21601935 | pmc = 3123404 | doi = 10.1016/j.tig.2011.04.002 }}</ref>

Some functional classes of genes are more likely to be bidirectionally paired than others. Genes implicated in DNA repair are five times more likely to be regulated by bidirectional promoters than by unidirectional promoters. [[Chaperone proteins]] are three times more likely, and [[mitochondrial gene]]s are more than twice as likely. Many basic [[Housekeeping gene|housekeeping]] and cellular metabolic genes are regulated by bidirectional promoters.<ref name="Trinklein" />
The overrepresentation of bidirectionally paired DNA repair genes associates these promoters with [[cancer]]. Forty-five percent of human [[Somatic (biology)|somatic]] [[oncogenes]] seem to be regulated by bidirectional promoters – significantly more than non-cancer causing genes. Hypermethylation of the promoters between gene pairs [[WNT9A]]/CD558500, [[CTDSPL]]/BC040563, and [[KCNK15]]/BF195580 has been associated with tumors.<ref name="Shu" />

Certain sequence characteristics have been observed in bidirectional promoters, including a lack of [[TATA box]]es, an abundance of [[CpG site|CpG islands]], and a symmetry around the midpoint of dominant Cs and As on one side and Gs and Ts on the other. A motif with the consensus sequence of TCTCGCGAGA, also called the [[CGCG element]], was recently shown to drive PolII-driven bidirectional transcription in CpG islands.<ref>{{cite journal | vauthors = Mahpour A, Scruggs BS, Smiraglia D, Ouchi T, Gelman IH | title = A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters | journal = PLOS ONE | volume = 13 | issue = 10 | pages = e0205608 | date = 2018-10-17 | pmid = 30332484 | pmc = 6192621 | doi = 10.1371/journal.pone.0205608 | doi-access = free | bibcode = 2018PLoSO..1305608M }}</ref> [[CCAAT box]]es are common, as they are in many promoters that lack TATA boxes. In addition, the [[Sequence motif|motifs]] NRF-1, [[GABPA]], [[YY1]], and ACTACAnnTCCC are represented in bidirectional promoters at significantly higher rates than in unidirectional promoters. The absence of TATA boxes in bidirectional promoters suggests that TATA boxes play a role in determining the directionality of promoters, but counterexamples of bidirectional promoters do possess TATA boxes and unidirectional promoters without them indicates that they cannot be the only factor.<ref>{{cite journal | vauthors = Lin JM, Collins PJ, Trinklein ND, Fu Y, Xi H, Myers RM, Weng Z | title = Transcription factor binding and modified histones in human bidirectional promoters | journal = Genome Research | volume = 17 | issue = 6 | pages = 818–827 | date = June 2007 | pmid = 17568000 | pmc = 1891341 | doi = 10.1101/gr.5623407 }}</ref>

Although the term "bidirectional promoter" refers specifically to promoter regions of [[mRNA]]-encoding genes, [[luciferase]] assays have shown that over half of human genes do not have a strong directional bias. Research suggests that [[non-coding RNAs]] are frequently associated with the promoter regions of mRNA-encoding genes. It has been hypothesized that the recruitment and initiation of [[RNA polymerase II]] usually begins bidirectionally, but divergent transcription is halted at a checkpoint later during elongation. Possible mechanisms behind this regulation include sequences in the promoter region, chromatin modification, and the spatial orientation of the DNA.<ref name="dx" />