Editing Gene expression (section)

===Transcriptional regulation===
{{main|Transcriptional regulation}}
[[File:Regulation of Lactose Metabolism in Prokaryotes.svg|thumb|When lactose is present in a prokaryote, it acts as an inducer and inactivates the repressor so that the genes for lactose metabolism can be transcribed.]]
[[Transcriptional regulation|Regulation of transcription]] can be broken down into three main routes of influence; genetic (direct interaction of a control factor with the gene), modulation interaction of a control factor with the transcription machinery and epigenetic (non-sequence changes in DNA structure that influence transcription).<ref>{{cite journal | vauthors = Lee TI, Young RA | title = Transcriptional regulation and its misregulation in disease | journal = Cell | volume = 152 | issue = 6 | pages = 1237–1251 | date = March 2013 | pmid = 23498934 | pmc = 3640494 | doi = 10.1016/j.cell.2013.02.014 }}</ref><ref>{{cite journal | vauthors = O'Connor L, Gilmour J, Bonifer C | title = The Role of the Ubiquitously Expressed Transcription Factor Sp1 in Tissue-specific Transcriptional Regulation and in Disease | journal = The Yale Journal of Biology and Medicine | volume = 89 | issue = 4 | pages = 513–525 | date = December 2016 | pmid = 28018142 | pmc = 5168829 }}</ref>

[[File:Lambda repressor 1LMB.png|thumb|185px|right|alt=Ribbon diagram of the lambda repressor dimer bound to DNA.|The [[Lambda phage#Repressor|lambda repressor]] transcription factor (green) binds as a dimer to [[Nucleic acid double helix|major groove]] of DNA target (red and blue) and disables initiation of transcription. From {{PDB|1LMB}}.]]

Direct interaction with DNA is the simplest and the most direct method by which a protein changes transcription levels.<ref>{{cite journal | vauthors = Yesudhas D, Batool M, Anwar MA, Panneerselvam S, Choi S | title = Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors | journal = Genes | volume = 8 | issue = 8 | pages = 192 | date = August 2017 | pmid = 28763006 | pmc = 5575656 | doi = 10.3390/genes8080192 | doi-access = free }}</ref> Genes often have several protein binding sites around the coding region with the specific function of regulating transcription.<ref>{{cite journal | vauthors = Wang G, Wang F, Huang Q, Li Y, Liu Y, Wang Y | title = Understanding Transcription Factor Regulation by Integrating Gene Expression and DNase I Hypersensitive Sites | journal = BioMed Research International | volume = 2015 | pages = 757530 | date = 2015 | pmid = 26425553 | pmc = 4573618 | doi = 10.1155/2015/757530 | doi-access = free }}</ref> There are many classes of regulatory DNA binding sites known as [[enhancer (genetics)|enhancer]]s, [[insulator (genetics)|insulator]]s and [[silencer (genetics)|silencer]]s.<ref>{{cite journal | vauthors = Kolovos P, Knoch TA, Grosveld FG, Cook PR, Papantonis A | title = Enhancers and silencers: an integrated and simple model for their function | journal = Epigenetics & Chromatin | volume = 5 | issue = 1 | pages = 1 | date = January 2012 | pmid = 22230046 | pmc = 3281776 | doi = 10.1186/1756-8935-5-1 | doi-access = free }}</ref> The mechanisms for regulating transcription are varied, from blocking key binding sites on the DNA for [[RNA polymerase]] to acting as an [[activator (genetics)|activator]] and promoting transcription by assisting RNA polymerase binding.<ref>{{cite journal | vauthors = Fuda NJ, Ardehali MB, Lis JT | title = Defining mechanisms that regulate RNA polymerase II transcription in vivo | journal = Nature | volume = 461 | issue = 7261 | pages = 186–192 | date = September 2009 | pmid = 19741698 | pmc = 2833331 | doi = 10.1038/nature08449 | bibcode = 2009Natur.461..186F }}</ref>

The activity of transcription factors is further modulated by intracellular signals causing protein post-translational modification including [[phosphorylation]], [[acetylation]], or [[glycosylation]].<ref>{{cite journal | vauthors = Filtz TM, Vogel WK, Leid M | title = Regulation of transcription factor activity by interconnected post-translational modifications | journal = Trends in Pharmacological Sciences | volume = 35 | issue = 2 | pages = 76–85 | date = February 2014 | pmid = 24388790 | pmc = 3954851 | doi = 10.1016/j.tips.2013.11.005 }}</ref> These changes influence a transcription factor's ability to bind, directly or indirectly, to promoter DNA, to recruit RNA polymerase, or to favor elongation of a newly synthesized RNA molecule.<ref>{{cite journal | vauthors = Hampsey M | title = Molecular genetics of the RNA polymerase II general transcriptional machinery | journal = Microbiology and Molecular Biology Reviews | volume = 62 | issue = 2 | pages = 465–503 | date = June 1998 | pmid = 9618449 | pmc = 98922 | doi = 10.1128/MMBR.62.2.465-503.1998 }}</ref>

The nuclear membrane in eukaryotes allows further regulation of transcription factors by the duration of their presence in the nucleus, which is regulated by reversible changes in their structure and by binding of other proteins.<ref name="pmid18937349">{{cite journal | vauthors = Veitia RA | title = One thousand and one ways of making functionally similar transcriptional enhancers | journal = BioEssays | volume = 30 | issue = 11–12 | pages = 1052–1057 | date = November 2008 | pmid = 18937349 | doi = 10.1002/bies.20849 }}</ref> Environmental stimuli or endocrine signals<ref name="pmid19182219">{{cite journal | vauthors = Nguyen T, Nioi P, Pickett CB | title = The Nrf2-antioxidant response element signaling pathway and its activation by oxidative stress | journal = The Journal of Biological Chemistry | volume = 284 | issue = 20 | pages = 13291–13295 | date = May 2009 | pmid = 19182219 | pmc = 2679427 | doi = 10.1074/jbc.R900010200 | doi-access = free }}</ref> may cause modification of regulatory proteins<ref name="pmid18937370">{{cite journal | vauthors = Paul S | title = Dysfunction of the ubiquitin-proteasome system in multiple disease conditions: therapeutic approaches | journal = BioEssays | volume = 30 | issue = 11–12 | pages = 1172–1184 | date = November 2008 | pmid = 18937370 | doi = 10.1002/bies.20852 | s2cid = 29422790 }}</ref> eliciting cascades of intracellular signals,<ref name="pmid19319914">{{cite journal | vauthors = Los M, Maddika S, Erb B, Schulze-Osthoff K | title = Switching Akt: from survival signaling to deadly response | journal = BioEssays | volume = 31 | issue = 5 | pages = 492–495 | date = May 2009 | pmid = 19319914 | pmc = 2954189 | doi = 10.1002/bies.200900005 }}</ref> which result in regulation of gene expression.

It has become apparent that there is a significant influence of non-DNA-sequence specific effects on transcription.<ref>{{cite journal | vauthors = Afek A, Sela I, Musa-Lempel N, Lukatsky DB | title = Nonspecific transcription-factor-DNA binding influences nucleosome occupancy in yeast | journal = Biophysical Journal | volume = 101 | issue = 10 | pages = 2465–2475 | date = November 2011 | pmid = 22098745 | pmc = 3218343 | doi = 10.1016/j.bpj.2011.10.012 | arxiv = 1111.4779 | bibcode = 2011BpJ...101.2465A }}</ref> These effects are referred to as [[Epigenetics|epigenetic]] and involve the higher order structure of DNA, non-sequence specific DNA binding proteins and chemical modification of DNA.<ref>{{cite journal | vauthors = Moosavi A, Motevalizadeh Ardekani A | title = Role of Epigenetics in Biology and Human Diseases | journal = Iranian Biomedical Journal | volume = 20 | issue = 5 | pages = 246–258 | date = November 2016 | pmid = 27377127 | pmc = 5075137 | doi = 10.22045/ibj.2016.01 }}</ref> In general epigenetic effects alter the accessibility of DNA to proteins and so modulate transcription.<ref>{{cite book | vauthors = Al Aboud NM, Tupper C, Jialal I | chapter = Genetics, Epigenetic Mechanism |date=2024 | title = StatPearls | chapter-url = http://www.ncbi.nlm.nih.gov/books/NBK532999/ |access-date=2024-06-12 |place=Treasure Island (FL) |publisher=StatPearls Publishing |pmid=30422591 }}</ref>

[[File:Nucleosome 1KX5 2.png|thumb|left|alt=A cartoon representation of the nucleosome structure.|In eukaryotes, DNA is organized in form of [[nucleosomes]]. Note how the DNA (blue and green) is tightly wrapped around the protein core made of [[histone]] [[octamer]] (ribbon coils), restricting access to the DNA. From {{PDB|1KX5}}.]]

In eukaryotes the structure of [[chromatin]], controlled by the [[histone code]], regulates access to DNA with significant impacts on the expression of genes in [[euchromatin]] and [[heterochromatin]] areas.<ref>{{cite book | vauthors = Miller JL, Grant PA | chapter = The Role of DNA Methylation and Histone Modifications in Transcriptional Regulation in Humans | series = Subcellular Biochemistry | title = Epigenetics: Development and Disease | volume = 61 | pages = 289–317 | date = 2013 | pmid = 23150256 | pmc = 6611551 | doi = 10.1007/978-94-007-4525-4_13 | isbn = 978-94-007-4524-7 }}</ref>

====Enhancers, transcription factors, mediator complex and DNA loops in mammalian transcription====
[[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 (genetics)|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 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 proteins (a complex consisting of about 26 proteins in an interacting structure) communicate regulatory signals from the enhancer DNA-bound transcription factors to the promoter.]]

Gene expression in mammals is regulated by many [[cis-regulatory element]]s, including [[Promoter (genetics)|core promoters and promoter-proximal elements]] that are located near the [[Eukaryotic transcription|transcription start sites]] of genes, [[Upstream and downstream (DNA)|upstream]] on the DNA (towards the 5' region of the [[sense strand]]). 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 = 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> 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 genome regions that regulate genes. 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> Multiple enhancers, each often 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 gene expression.<ref name=Schoenfelder />

The illustration shows an enhancer looping around to come into 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]]). One member of the dimer is anchored to its binding motif on the enhancer and the other member is 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 = 1573–1588.e28 | date = December 2017 | pmid = 29224777 | pmc = 5785279 | doi = 10.1016/j.cell.2017.11.008 }}</ref> Several cell function-specific transcription factors (among the 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 | 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 | doi-access = free | bibcode = 2018PNAS..115E7222G }}</ref> A small combination of these enhancer-bound transcription factors, when brought close to a promoter by a DNA loop, govern transcription level of the target gene. 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 = 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 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 | 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>