Editing Gene expression (section)

==Regulation of gene expression==
{{main|Regulation of gene expression}}
[[File:Tortie-flame.jpg|thumb|right|alt=A cat with patches of orange and black fur. |The patchy colours of a [[tortoiseshell cat]] are the result of different levels of expression of [[biological pigment|pigmentation]] genes in different areas of the [[skin]].]]

Regulation of gene expression is the control of the amount and timing of appearance of the functional product of a gene. Control of expression is vital to allow a cell to produce the gene products it needs when it needs them; in turn, this gives cells the flexibility to adapt to a variable environment, external signals, damage to the cell, and other stimuli. More generally, gene regulation gives the cell control over all structure and function, and is the basis for [[cellular differentiation]], [[morphogenesis]] and the versatility and adaptability of any organism.

Numerous terms are used to describe types of genes depending on how they are regulated; these include:
* A '''constitutive gene'''<!--Bolded per MOS:BOLD because the phrase redirects here--> is a gene that is transcribed continually as opposed to a facultative gene, which is only transcribed when needed.
* A ''[[housekeeping gene]]'' is a gene that is required to maintain basic cellular function and so is typically expressed in all cell types of an organism. Examples include [[actin]], [[GAPDH]] and [[ubiquitin]]. Some housekeeping genes are transcribed at a relatively constant rate and these genes can be used as a reference point in experiments to measure the expression rates of other genes.
* A '''facultative gene'''<!--Bolded per MOS:BOLD because the phrase redirects here--> is a gene only transcribed when needed as opposed to a constitutive gene.
* An '''inducible gene'''<!--Bolded per MOS:BOLD because the phrase redirects here--> is a gene whose expression is either responsive to environmental change or dependent on the position in the cell cycle.

Any step of gene expression may be modulated, from the DNA-RNA transcription step to [[post-translational modification]] of a protein. The stability of the final gene product, whether it is RNA or protein, also contributes to the expression level of the gene—an unstable product results in a low expression level. In general gene expression is regulated through changes<ref name="pmid15277516">{{cite journal | vauthors = Zaidi SK, Young DW, Choi JY, Pratap J, Javed A, Montecino M, Stein JL, Lian JB, van Wijnen AJ, Stein GS | title = Intranuclear trafficking: organization and assembly of regulatory machinery for combinatorial biological control | journal = The Journal of Biological Chemistry | volume = 279 | issue = 42 | pages = 43363–43366 | date = October 2004 | pmid = 15277516 | doi = 10.1074/jbc.R400020200 | doi-access = free }}</ref> in the number and type of interactions between molecules<ref name="pmid19154003">{{cite journal | vauthors = Mattick JS, Amaral PP, Dinger ME, Mercer TR, Mehler MF | title = RNA regulation of epigenetic processes | journal = BioEssays | volume = 31 | issue = 1 | pages = 51–59 | date = January 2009 | pmid = 19154003 | doi = 10.1002/bies.080099 | doi-access = free }}</ref> that collectively influence transcription of DNA<ref name="pmid19274664">{{cite journal | vauthors = Martinez NJ, Walhout AJ | title = The interplay between transcription factors and microRNAs in genome-scale regulatory networks | journal = BioEssays | volume = 31 | issue = 4 | pages = 435–445 | date = April 2009 | pmid = 19274664 | pmc = 3118512 | doi = 10.1002/bies.200800212 }}</ref> and translation of RNA.<ref name="pmid18348251">{{cite journal | vauthors = Tomilin NV | title = Regulation of mammalian gene expression by retroelements and non-coding tandem repeats | journal = BioEssays | volume = 30 | issue = 4 | pages = 338–348 | date = April 2008 | pmid = 18348251 | doi = 10.1002/bies.20741 | doi-access = free }}</ref>

Some simple examples of where gene expression is important are:
* Control of [[insulin]] expression so it gives a signal for [[blood glucose regulation]].
* [[X-inactivation|X chromosome inactivation]] in female [[mammals]] to prevent an "overdose" of the genes it contains.
* [[Cyclin]] expression levels control progression through the eukaryotic [[cell cycle]].

===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>

===DNA methylation and demethylation in transcriptional regulation===

[[File:DNA methylation.svg|thumb|300px|DNA methylation is the addition of a [[methyl]] 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]].]]

[[DNA methylation]] is a widespread mechanism for epigenetic influence on gene expression and is seen in [[bacteria]] and [[eukaryotes]] and has roles in heritable transcription silencing and transcription regulation. Methylation most often occurs on a cytosine (see Figure). Methylation of cytosine primarily occurs in dinucleotide sequences where a cytosine is followed by a guanine, a [[CpG site]]. The number of [[CpG site]]s in the human genome is about 28 million.<ref name="pmid26932361">{{cite journal | vauthors = Lövkvist C, Dodd IB, Sneppen K, Haerter JO | title = DNA methylation in human epigenomes depends on local topology of CpG sites | journal = Nucleic Acids Research | volume = 44 | issue = 11 | pages = 5123–5132 | date = June 2016 | pmid = 26932361 | pmc = 4914085 | doi = 10.1093/nar/gkw124 }}</ref> Depending on the type of cell, about 70% of the CpG sites have a methylated cytosine.<ref name="Jabbari2004">{{cite journal | vauthors = Jabbari K, Bernardi G | title = Cytosine methylation and CpG, TpG (CpA) and TpA frequencies | journal = Gene | volume = 333 | pages = 143–149 | date = May 2004 | pmid = 15177689 | doi = 10.1016/j.gene.2004.02.043 }}</ref>

Methylation of cytosine in DNA has a major role in regulating gene expression. Methylation of CpGs in a promoter region of a gene usually represses gene transcription<ref name="pmid17334365">{{cite journal | vauthors = Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M, Schübeler D | title = Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome | journal = Nature Genetics | volume = 39 | issue = 4 | pages = 457–466 | date = April 2007 | pmid = 17334365 | doi = 10.1038/ng1990 | s2cid = 22446734 }}</ref> while methylation of CpGs in the body of a gene increases expression.<ref name="pmid25263941">{{cite journal | vauthors = Yang X, Han H, De Carvalho DD, Lay FD, Jones PA, Liang G | title = Gene body methylation can alter gene expression and is a therapeutic target in cancer | journal = Cancer Cell | volume = 26 | issue = 4 | pages = 577–590 | date = October 2014 | pmid = 25263941 | pmc = 4224113 | doi = 10.1016/j.ccr.2014.07.028 }}</ref> [[TET enzymes]] play a central role in demethylation of methylated cytosines. Demethylation of CpGs in a gene promoter by [[TET enzymes|TET enzyme]] activity increases transcription of the gene.<ref name="pmid24108092">{{cite journal | vauthors = Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D, Bernstein BE, Costello JF, Wilkinson MF, Joung JK | title = Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins | journal = Nature Biotechnology | volume = 31 | issue = 12 | pages = 1137–1142 | date = December 2013 | pmid = 24108092 | pmc = 3858462 | doi = 10.1038/nbt.2726 }}</ref>

===Transcriptional regulation in learning and memory===
{{main|Epigenetics in learning and memory}}

[[File:Brain regions involved in memory formation.jpg|thumb|400 px|The identified areas of the human brain are involved in memory formation.]]

In a rat, contextual [[fear conditioning]] (CFC) is a painful learning experience. Just one episode of CFC can result in a life-long fearful memory.<ref name=KimJung>{{cite journal | vauthors = Kim JJ, Jung MW | title = Neural circuits and mechanisms involved in Pavlovian fear conditioning: a critical review | journal = Neuroscience and Biobehavioral Reviews | volume = 30 | issue = 2 | pages = 188–202 | date = 2006 | pmid = 16120461 | pmc = 4342048 | doi = 10.1016/j.neubiorev.2005.06.005 }}</ref> After an episode of CFC, cytosine methylation is altered in the promoter regions of about 9.17% of all genes in the [[hippocampus]] neuron DNA of a rat.<ref name=DukeSweatt>{{cite journal | vauthors = Duke CG, Kennedy AJ, Gavin CF, Day JJ, Sweatt JD | title = Experience-dependent epigenomic reorganization in the hippocampus | journal = Learning & Memory | volume = 24 | issue = 7 | pages = 278–288 | date = July 2017 | pmid = 28620075 | pmc = 5473107 | doi = 10.1101/lm.045112.117 }}</ref> The [[hippocampus]] is where new memories are initially stored. After CFC about 500 genes have increased transcription (often due to demethylation of CpG sites in a promoter region) and about 1,000 genes have decreased transcription (often due to newly formed 5-methylcytosine at CpG sites in a promoter region). The pattern of induced and repressed genes within neurons appears to provide a molecular basis for forming the first transient memory of this training event in the hippocampus of the rat brain.<ref name=DukeSweatt />

Some specific mechanisms guiding new DNA methylations and new [[DNA demethylation]]s in the [[hippocampus]] during memory establishment have been established (see<ref name=Bernstein>{{cite journal | vauthors = Bernstein C | title = DNA Methylation and Establishing Memory | journal = Epigenetics Insights | volume = 15 | issue =  | pages = 25168657211072499 | date = 2022 | pmid = 35098021 | pmc = 8793415 | doi = 10.1177/25168657211072499 }}</ref> for summary).  One mechanism includes guiding the short isoform of the [[Tet methylcytosine dioxygenase 1|TET1]] [[DNA demethylation]] enzyme, TET1s, to about 600 locations on the genome.  The guidance is performed by association of TET1s with [[EGR1]] protein, a transcription factor important in memory formation.  Bringing TET1s to these locations initiates DNA demethylation at those sites, up-regulating associated genes. A second mechanism involves DNMT3A2, a splice-isoform of [[DNA methyltransferase]] DNMT3A, which adds methyl groups to cytosines in DNA.  This isoform is induced by synaptic activity, and its location of action appears to be determined by [[histone]] post-translational modifications (a [[histone code]]).  The resulting new [[messenger RNA]]s are then transported by [[messenger RNP]] particles (neuronal granules) to synapses of the neurons, where they can be translated into proteins affecting the activities of synapses.<ref name=Bernstein />

In particular, the [[brain-derived neurotrophic factor]] gene (''BDNF'') is known as a "learning gene".<ref name=Keifer>{{cite journal | vauthors = Keifer J | title = Primetime for Learning Genes | journal = Genes | volume = 8 | issue = 2 | page = 69 | date = February 2017 | pmid = 28208656 | pmc = 5333058 | doi = 10.3390/genes8020069 | doi-access = free }}</ref> After CFC there was upregulation of ''BDNF'' gene expression, related to decreased CpG methylation of certain internal promoters of the gene, and this was correlated with learning.<ref name=Keifer />

===Transcriptional regulation in cancer===
{{main|Regulation of transcription in cancer}}

The majority of gene [[Promoter (genetics)#CpG islands in promoters|promoters]] contain a [[CpG site#CpG islands|CpG island]] with numerous [[CpG site]]s.<ref name="pmid16432200">{{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 = Proceedings of the National Academy of Sciences of the United States of America | volume = 103 | issue = 5 | pages = 1412–1417 | date = January 2006 | pmid = 16432200 | pmc = 1345710 | doi = 10.1073/pnas.0510310103 | doi-access = free | bibcode = 2006PNAS..103.1412S }}</ref> When many of a gene's promoter CpG sites are [[DNA methylation|methylated]] the gene becomes silenced.<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> Colorectal cancers typically have 3 to 6 [[Somatic evolution in cancer#Glossary|driver]] mutations and 33 to 66 [[Genetic hitchhiking|hitchhiker]] or passenger mutations.<ref name="pmid23539594">{{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 = 1546–1558 | date = March 2013 | pmid = 23539594 | pmc = 3749880 | doi = 10.1126/science.1235122 | bibcode = 2013Sci...339.1546V }}</ref> 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 [[Cancer epigenetics|epigenetic]] mechanisms, such as altered expression of [[MicroRNA#DNA repair and cancer|microRNAs]].<ref name="pmid24616890">{{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 = International Journal of Genomics | volume = 2014 | pages = 820248 | year = 2014 | pmid = 24616890 | pmc = 3926391 | doi = 10.1155/2014/820248 | doi-access = free }}</ref> In breast cancer, transcriptional repression of [[BRCA1]] may occur more frequently by over-transcribed microRNA-182 than by hypermethylation of the BRCA1 promoter (see [[BRCA1#Low expression of BRCA1 in breast and ovarian cancers|Low expression of BRCA1 in breast and ovarian cancers]]).

===Post-transcriptional regulation===
{{main|Post-transcriptional regulation}}
In eukaryotes, where export of RNA is required before translation is possible, nuclear export is thought to provide additional control over gene expression. All transport in and out of the nucleus is via the [[nuclear pore]] and transport is controlled by a wide range of [[importin]] and [[exportin]] proteins.<ref>{{cite journal | vauthors = De Magistris P | title = The Great Escape: mRNA Export through the Nuclear Pore Complex | journal = International Journal of Molecular Sciences | volume = 22 | issue = 21 | pages = 11767 | date = October 2021 | pmid = 34769195 | pmc = 8583845 | doi = 10.3390/ijms222111767 | doi-access = free }}</ref>

Expression of a gene coding for a protein is only possible if the messenger RNA carrying the code survives long enough to be translated.<ref name=":0">{{Citation | vauthors =  Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P |title=From RNA to Protein |date=2002 |work=Molecular Biology of the Cell. 4th edition |url=https://www.ncbi.nlm.nih.gov/books/NBK26829/ |access-date=2024-06-10 |publisher=Garland Science |language=en }}</ref> In a typical cell, an RNA molecule is only stable if specifically protected from degradation.<ref>{{cite journal | vauthors = Liu H, Luo M, Wen JK | title = mRNA stability in the nucleus | journal = Journal of Zhejiang University. Science. B | volume = 15 | issue = 5 | pages = 444–454 | date = May 2014 | pmid = 24793762 | pmc = 4076601 | doi = 10.1631/jzus.B1400088 }}</ref> RNA degradation has particular importance in regulation of expression in eukaryotic cells where mRNA has to travel significant distances before being translated.<ref>{{cite journal | vauthors = Yan LL, Zaher HS | title = How do cells cope with RNA damage and its consequences? | journal = The Journal of Biological Chemistry | volume = 294 | issue = 41 | pages = 15158–15171 | date = October 2019 | pmid = 31439666 | pmc = 6791314 | doi = 10.1074/jbc.REV119.006513 | doi-access = free }}</ref> In eukaryotes, RNA is stabilised by certain post-transcriptional modifications, particularly the [[5′ cap]] and [[polyadenylation|poly-adenylated tail]].<ref>{{cite journal | vauthors = Passmore LA, Coller J | title = Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression | journal = Nature Reviews. Molecular Cell Biology | volume = 23 | issue = 2 | pages = 93–106 | date = February 2022 | pmid = 34594027 | pmc = 7614307 | doi = 10.1038/s41580-021-00417-y }}</ref>

Intentional degradation of mRNA is used not just as a defence mechanism from foreign RNA (normally from viruses) but also as a route of mRNA ''destabilisation''.<ref>{{cite journal | vauthors = Shehata SI, Watkins JM, Burke JM, Parker R | title = Mechanisms and consequences of mRNA destabilization during viral infections | journal = Virology Journal | volume = 21 | issue = 1 | pages = 38 | date = February 2024 | pmid = 38321453 | pmc = 10848536 | doi = 10.1186/s12985-024-02305-1 | doi-access = free }}</ref> If an mRNA molecule has a complementary sequence to a [[small interfering RNA]] then it is targeted for destruction via the [[RNA interference]] pathway.<ref>{{cite journal | vauthors = Tang L, Chen HY, Hao NB, Tang B, Guo H, Yong X, Dong H, Yang SM | title = microRNA inhibitors: Natural and artificial sequestration of microRNA | journal = Cancer Letters | volume = 407 | pages = 139–147 | date = October 2017 | pmid = 28602827 | pmc = 7152241 | doi = 10.1016/B978-0-444-64046-8.00282-2 | isbn = 978-0-444-64047-5 }}</ref>

===Three prime untranslated regions and microRNAs===
{{main|Three prime untranslated region}}
{{main|MicroRNA}}
[[Three prime untranslated region]]s (3′UTRs) of [[messenger RNA]]s (mRNAs) often contain regulatory sequences that post-transcriptionally influence gene expression. Such 3′-UTRs often contain both binding sites for [[microRNA]]s (miRNAs) as well as for regulatory proteins.<ref>{{cite journal | vauthors = Mayr C | title = What Are 3' UTRs Doing? | journal = Cold Spring Harbor Perspectives in Biology | volume = 11 | issue = 10 | pages = a034728 | date = October 2019 | pmid = 30181377 | pmc = 6771366 | doi = 10.1101/cshperspect.a034728 }}</ref> By binding to specific sites within the 3′-UTR, miRNAs can decrease gene expression of various mRNAs by either inhibiting translation or directly causing degradation of the transcript.<ref>{{cite journal | vauthors = O'Brien J, Hayder H, Zayed Y, Peng C | title = Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation | journal = Frontiers in Endocrinology | volume = 9 | pages = 402 | date = 2018-08-03 | pmid = 30123182 | pmc = 6085463 | doi = 10.3389/fendo.2018.00402 | doi-access = free }}</ref> The 3′-UTR also may have silencer regions that bind repressor proteins that inhibit the expression of a mRNA.<ref>{{cite journal | vauthors = Mayya VK, Duchaine TF | title = Ciphers and Executioners: How 3'-Untranslated Regions Determine the Fate of Messenger RNAs | journal = Frontiers in Genetics | volume = 10 | pages = 6 | date = 2019-01-24 | pmid = 30740123 | pmc = 6357968 | doi = 10.3389/fgene.2019.00006 | doi-access = free }}</ref>

The 3′-UTR often contains [[Three prime untranslated region#MicroRNA response elements|microRNA response elements (MREs)]]. MREs are sequences to which miRNAs bind. These are prevalent motifs within 3′-UTRs. Among all regulatory motifs within the 3′-UTRs (e.g. including silencer regions), MREs make up about half of the motifs.<ref>{{cite journal | vauthors = Nair AA, Tang X, Thompson KJ, Vedell PT, Kalari KR, Subramanian S | title = Frequency of MicroRNA Response Elements Identifies Pathologically Relevant Signaling Pathways in Triple-Negative Breast Cancer | journal = iScience | volume = 23 | issue = 6 | pages = 101249 | date = June 2020 | pmid = 32629614 | pmc = 7322352 | doi = 10.1016/j.isci.2020.101249 | bibcode = 2020iSci...23j1249N }}</ref>

As of 2014, the [[miRBase]] web site,<ref>miRBase.org</ref> an archive of [[microRNA|miRNA]] [[Sequence (biology)|sequences]] and annotations, listed 28,645 entries in 233 biologic species. Of these, 1,881 miRNAs were in annotated human miRNA loci. miRNAs were predicted to have an average of about four hundred target [[messenger RNA|mRNAs]] (affecting expression of several hundred genes).<ref name=Friedman>{{cite journal | vauthors = Friedman RC, Farh KK, Burge CB, Bartel DP | title = Most mammalian mRNAs are conserved targets of microRNAs | journal = Genome Research | volume = 19 | issue = 1 | pages = 92–105 | date = January 2009 | pmid = 18955434 | pmc = 2612969 | doi = 10.1101/gr.082701.108 }}</ref> Friedman et al.<ref name=Friedman /> estimate that >45,000 miRNA target sites within human mRNA 3′UTRs are conserved above background levels, and >60% of human protein-coding genes have been under selective pressure to maintain pairing to miRNAs.

Direct experiments show that a single miRNA can reduce the stability of hundreds of unique mRNAs.<ref name="pmid15685193">{{cite journal | vauthors = Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM | title = Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs | journal = Nature | volume = 433 | issue = 7027 | pages = 769–773 | date = February 2005 | pmid = 15685193 | doi = 10.1038/nature03315 | s2cid = 4430576 | bibcode = 2005Natur.433..769L }}</ref> Other experiments show that a single miRNA may repress the production of hundreds of proteins, but that this repression often is relatively mild (less than 2-fold).<ref>{{cite journal | vauthors = Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N | title = Widespread changes in protein synthesis induced by microRNAs | journal = Nature | volume = 455 | issue = 7209 | pages = 58–63 | date = September 2008 | pmid = 18668040 | doi = 10.1038/nature07228 | s2cid = 4429008 | bibcode = 2008Natur.455...58S }}</ref><ref>{{cite journal | vauthors = Baek D, Villén J, Shin C, Camargo FD, Gygi SP, Bartel DP | title = The impact of microRNAs on protein output | journal = Nature | volume = 455 | issue = 7209 | pages = 64–71 | date = September 2008 | pmid = 18668037 | pmc = 2745094 | doi = 10.1038/nature07242 | bibcode = 2008Natur.455...64B }}</ref>

The effects of miRNA dysregulation of gene expression seem to be important in cancer.<ref name="pmid21931505">{{cite journal | vauthors = Palmero EI, de Campos SG, Campos M, de Souza NC, Guerreiro ID, Carvalho AL, Marques MM | title = Mechanisms and role of microRNA deregulation in cancer onset and progression | journal = Genetics and Molecular Biology | volume = 34 | issue = 3 | pages = 363–370 | date = July 2011 | pmid = 21931505 | pmc = 3168173 | doi = 10.1590/S1415-47572011000300001 }}</ref> For instance, in gastrointestinal cancers, nine miRNAs have been identified as [[Epigenetics|epigenetically]] altered and effective in down regulating DNA repair enzymes.<ref name="pmid25987950">{{cite journal | vauthors = Bernstein C, Bernstein H | title = Epigenetic reduction of DNA repair in progression to gastrointestinal cancer | journal = World Journal of Gastrointestinal Oncology | volume = 7 | issue = 5 | pages = 30–46 | date = May 2015 | pmid = 25987950 | pmc = 4434036 | doi = 10.4251/wjgo.v7.i5.30 | doi-access = free }}</ref>

The effects of miRNA dysregulation of gene expression also seem to be important in neuropsychiatric disorders, such as schizophrenia, bipolar disorder, major depression, Parkinson's disease, Alzheimer's disease and autism spectrum disorders.<ref name="pmid22539927">{{cite journal | vauthors = Mellios N, Sur M | title = The Emerging Role of microRNAs in Schizophrenia and Autism Spectrum Disorders | journal = Frontiers in Psychiatry | volume = 3 | pages = 39 | year = 2012 | pmid = 22539927 | pmc = 3336189 | doi = 10.3389/fpsyt.2012.00039 | doi-access = free }}</ref><ref name="pmid25636176">{{cite journal | vauthors = Geaghan M, Cairns MJ | title = MicroRNA and Posttranscriptional Dysregulation in Psychiatry | journal = Biological Psychiatry | volume = 78 | issue = 4 | pages = 231–239 | date = August 2015 | pmid = 25636176 | doi = 10.1016/j.biopsych.2014.12.009 | hdl-access = free | doi-access = free | hdl = 1959.13/1335073 }}</ref>

===Translational regulation===
[[File:Neomycin B C.svg|thumb|right|alt=A chemical structure of neomycin molecule.|[[Neomycin]] is an example of a small molecule that reduces expression of all protein genes inevitably leading to cell death; it thus acts as an [[antibiotic]].]]

{{Main|Translation (genetics)}}
Direct regulation of translation is less prevalent than control of transcription or mRNA stability but is occasionally used.<ref>{{cite journal | vauthors = Sonenberg N, Hinnebusch AG | title = Regulation of translation initiation in eukaryotes: mechanisms and biological targets | journal = Cell | volume = 136 | issue = 4 | pages = 731–745 | date = February 2009 | pmid = 19239892 | pmc = 3610329 | doi = 10.1016/j.cell.2009.01.042 }}</ref> Inhibition of protein translation is a major target for [[toxin]]s and [[antibiotic]]s, so they can kill a cell by overriding its normal gene expression control.<ref>{{cite journal | vauthors = Jurėnas D, Van Melderen L | title = The Variety in the Common Theme of Translation Inhibition by Type II Toxin-Antitoxin Systems | journal = Frontiers in Genetics | volume = 11 | pages = 262 | date = 2020-04-17 | pmid = 32362907 | pmc = 7180214 | doi = 10.3389/fgene.2020.00262 | doi-access = free }}</ref> [[Protein synthesis inhibitor]]s include the antibiotic [[neomycin]] and the toxin [[ricin]].<ref>{{cite journal | vauthors = Dmitriev SE, Vladimirov DO, Lashkevich KA | title = A Quick Guide to Small-Molecule Inhibitors of Eukaryotic Protein Synthesis | journal = Biochemistry. Biokhimiia | volume = 85 | issue = 11 | pages = 1389–1421 | date = November 2020 | pmid = 33280581 | pmc = 7689648 | doi = 10.1134/S0006297920110097 }}</ref>

===Post-translational modifications===
{{Main|Post-translational modification}}
Post-translational modifications (PTMs) are [[covalent]] modifications to proteins. Like RNA splicing, they help to significantly diversify the proteome. These modifications are usually catalyzed by enzymes. Additionally, processes like covalent additions to amino acid side chain residues can often be reversed by other enzymes. However, some, like the [[proteolysis|proteolytic cleavage]] of the protein backbone, are irreversible.<ref name="WalshGarneau-Tsodikova2005">{{cite journal | vauthors = Walsh CT, Garneau-Tsodikova S, Gatto GJ | title = Protein posttranslational modifications: the chemistry of proteome diversifications | journal = Angewandte Chemie | volume = 44 | issue = 45 | pages = 7342–7372 | date = December 2005 | pmid = 16267872 | doi = 10.1002/anie.200501023 | s2cid = 32157563 }}</ref>

PTMs play many important roles in the cell.<ref name="KhouryBaliban2011">{{cite journal | vauthors = Khoury GA, Baliban RC, Floudas CA | title = Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database | journal = Scientific Reports | volume = 1 | pages = 90 | date = September 2011 | pmid = 22034591 | pmc = 3201773 | doi = 10.1038/srep00090 | number = 90 | author-link3 = Christodoulos Floudas | bibcode = 2011NatSR...1...90K }}</ref> For example, phosphorylation is primarily involved in activating and deactivating proteins and in signaling pathways.<ref name="MannJensen2003">{{cite journal | vauthors = Mann M, Jensen ON | title = Proteomic analysis of post-translational modifications | journal = Nature Biotechnology | volume = 21 | issue = 3 | pages = 255–261 | date = March 2003 | pmid = 12610572 | doi = 10.1038/nbt0303-255 | s2cid = 205266061 }}</ref> PTMs are involved in transcriptional regulation: an important function of acetylation and methylation is histone tail modification, which alters how accessible DNA is for transcription.<ref name="WalshGarneau-Tsodikova2005"/> They can also be seen in the immune system, where glycosylation plays a key role.<ref name="SeoLee2004">{{cite journal | vauthors = Seo J, Lee KJ | title = Post-translational modifications and their biological functions: proteomic analysis and systematic approaches | journal = Journal of Biochemistry and Molecular Biology | volume = 37 | issue = 1 | pages = 35–44 | date = January 2004 | pmid = 14761301 | doi = 10.5483/bmbrep.2004.37.1.035 | doi-access = free }}</ref> One type of PTM can initiate another type of PTM, as can be seen in how [[ubiquitination]] tags proteins for degradation through proteolysis.<ref name="WalshGarneau-Tsodikova2005"/> Proteolysis, other than being involved in breaking down proteins, is also important in activating and deactivating them, and in regulating biological processes such as DNA transcription and cell death.<ref name="RogersOverall2013">{{cite journal | vauthors = Rogers LD, Overall CM | title = Proteolytic post-translational modification of proteins: proteomic tools and methodology | journal = Molecular & Cellular Proteomics | volume = 12 | issue = 12 | pages = 3532–3542 | date = December 2013 | pmid = 23887885 | pmc = 3861706 | doi = 10.1074/mcp.M113.031310 | doi-access = free }}</ref>