Editing MicroRNA (section)

==RNA-induced silencing complex==
{{Main|RNA-induced silencing complex}}

The mature miRNA is part of an active RNA-induced silencing complex (RISC) containing Dicer and many associated proteins.<ref name=Rana>{{cite journal | vauthors = Rana TM | title = Illuminating the silence: understanding the structure and function of small RNAs | journal = Nature Reviews Molecular Cell Biology | volume = 8 | issue = 1 | pages = 23–36 | date = January 2007 | pmid = 17183358 | doi = 10.1038/nrm2085 | s2cid = 8966239 }}</ref> RISC is also known as a microRNA ribonucleoprotein complex (miRNP);<ref name="pmid12000786">{{cite journal | vauthors = Schwarz DS, Zamore PD | title = Why do miRNAs live in the miRNP? | journal = Genes & Development | volume = 16 | issue = 9 | pages = 1025–31 | date = May 2002 | pmid = 12000786 | doi = 10.1101/gad.992502 | doi-access = free }}</ref> A RISC with incorporated miRNA is sometimes referred to as a "miRISC."

Dicer processing of the pre-miRNA is thought to be coupled with unwinding of the duplex. Generally, only one strand is incorporated into the miRISC, selected on the basis of its thermodynamic instability and weaker base-pairing on the 5' end relative to the other strand.<ref name="pmid15292246">{{cite journal | vauthors = Krol J, Sobczak K, Wilczynska U, Drath M, Jasinska A, Kaczynska D, Krzyzosiak WJ | title = Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design | journal = The Journal of Biological Chemistry | volume = 279 | issue = 40 | pages = 42230–39 | date = October 2004 | pmid = 15292246 | doi = 10.1074/jbc.M404931200 | doi-access = free }}</ref><ref name="pmid14567918">{{cite journal | vauthors = Khvorova A, Reynolds A, Jayasena SD | title = Functional siRNAs and miRNAs exhibit strand bias | journal = Cell | volume = 115 | issue = 2 | pages = 209–16 | date = October 2003 | pmid = 14567918 | doi = 10.1016/S0092-8674(03)00801-8 | doi-access = free }}</ref><ref name="pmid14567917">{{cite journal | vauthors = Schwarz DS, Hutvágner G, Du T, Xu Z, Aronin N, Zamore PD | title = Asymmetry in the assembly of the RNAi enzyme complex | journal = Cell | volume = 115 | issue = 2 | pages = 199–208 | date = October 2003 | pmid = 14567917 | doi = 10.1016/S0092-8674(03)00759-1 | doi-access = free }}</ref> The position of the hairpin may also influence strand choice.<ref name="pmid16005165">{{cite journal | vauthors = Lin SL, Chang D, Ying SY | title = Asymmetry of intronic pre-miRNA structures in functional RISC assembly | journal = Gene | volume = 356 | pages = 32–38 | date = August 2005 | pmid = 16005165 | pmc = 1788082 | doi = 10.1016/j.gene.2005.04.036 }}</ref> The other strand, called the passenger strand due to its lower levels in the steady state, is denoted with an asterisk (*) and is normally degraded. In some cases, both strands of the duplex are viable and become functional miRNA that target different mRNA populations.<ref name="pmid18769156">{{cite journal | vauthors = Okamura K, Chung WJ, Lai EC | title = The long and short of inverted repeat genes in animals: microRNAs, mirtrons and hairpin RNAs | journal = Cell Cycle | volume = 7 | issue = 18 | pages = 2840–45 | date = September 2008 | pmid = 18769156 | pmc = 2697033 | doi = 10.4161/cc.7.18.6734 }}</ref>

[[File:MicroRNAs and Argonaute RNA binding.svg|thumb|right|AGO2 (grey) in complex with a microRNA (light blue) and its target mRNA (dark blue)]]

Members of the [[Argonaute]] (Ago) protein family are central to RISC function. Argonautes are needed for miRNA-induced silencing and contain two conserved RNA binding domains: a PAZ domain that can bind the single stranded 3' end of the mature miRNA and a [[Piwi|PIWI]] domain that structurally resembles [[Ribonuclease H|ribonuclease-H]] and functions to interact with the 5' end of the guide strand. They bind the mature miRNA and orient it for interaction with a target mRNA. Some argonautes, for example human Ago2, cleave target transcripts directly; argonautes may also recruit additional proteins to achieve translational repression.<ref name=Pratt>{{cite journal | vauthors = Pratt AJ, MacRae IJ | title = The RNA-induced silencing complex: a versatile gene-silencing machine | journal = The Journal of Biological Chemistry | volume = 284 | issue = 27 | pages = 17897–901 | date = July 2009 | pmid = 19342379 | pmc = 2709356 | doi = 10.1074/jbc.R900012200 | doi-access = free }}</ref> The human genome encodes eight argonaute proteins divided by sequence similarities into two families: AGO (with four members present in all mammalian cells and called E1F2C/hAgo in humans), and PIWI (found in the germline and hematopoietic stem cells).<ref name="pmid12000786"/><ref name=Pratt/>

Additional RISC components include [[TARBP2|TRBP]] [human immunodeficiency virus (HIV) transactivating response RNA (TAR) binding protein],<ref name="pmid18178619">{{cite journal | vauthors = MacRae IJ, Ma E, Zhou M, Robinson CV, Doudna JA | title = In vitro reconstitution of the human RISC-loading complex | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 2 | pages = 512–17 | date = January 2008 | pmid = 18178619 | pmc = 2206567 | doi = 10.1073/pnas.0710869105 | bibcode = 2008PNAS..105..512M | doi-access = free }}</ref> PACT (protein activator of the [[interferon]]-induced [[protein kinase]]), the SMN complex, [[Fragile X syndrome|fragile X mental retardation protein]] (FMRP), Tudor staphylococcal nuclease-domain-containing protein (Tudor-SN), the putative DNA [[helicase]] [[MOV10]], and the RNA recognition motif containing protein [[TNRC6B]].<ref name="pmid15145345"/><ref name="pmid11914277">{{cite journal | vauthors = Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, [[Juri Rappsilber|Rappsilber J]], Mann M, Dreyfuss G | title = miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs | journal = Genes & Development | volume = 16 | issue = 6 | pages = 720–78 | date = March 2002 | pmid = 11914277 | pmc = 155365 | doi = 10.1101/gad.974702 }}</ref><ref>{{cite journal | vauthors = Meister G, Landthaler M, Peters L, Chen PY, Urlaub H, Lührmann R, Tuschl T | title = Identification of novel argonaute-associated proteins | journal = Current Biology | volume = 15 | issue = 23 | pages = 2149–55 | date = December 2005 | pmid = 16289642 | doi = 10.1016/j.cub.2005.10.048 | doi-access = free | bibcode = 2005CBio...15.2149M | hdl = 11858/00-001M-0000-0012-E763-B | hdl-access = free }}</ref>

===Mode of silencing and regulatory loops===
Gene silencing may occur either via mRNA degradation or preventing mRNA from being translated. For example, miR16 contains a sequence complementary to the [[AU-rich element]]<ref>{{Cite journal |last1=Shaw |first1=G. |last2=Kamen |first2=R. |date=1986-08-29 |title=A conserved AU sequence from the 3' untranslated region of GM-CSF mRNA mediates selective mRNA degradation |url=https://pubmed.ncbi.nlm.nih.gov/3488815/ |journal=Cell |volume=46 |issue=5 |pages=659–667 |doi=10.1016/0092-8674(86)90341-7 |issn=0092-8674 |pmid=3488815}}</ref> found in the 3'UTR of many unstable mRNAs, such as [[Tumor necrosis factor alpha|TNF alpha]] or [[Granulocyte macrophage colony-stimulating factor|GM-CSF]].<ref name="Jing Q, Huang S, Guth S, Zarubin T, Motoyama A, Chen J, Di Padova F, Lin SC, Gram H, Han J 2005 623-34">{{cite journal | vauthors = Jing Q, Huang S, Guth S, Zarubin T, Motoyama A, Chen J, Di Padova F, Lin SC, Gram H, Han J | title = Involvement of microRNA in AU-rich element-mediated mRNA instability | journal = Cell | volume = 120 | issue = 5 | pages = 623–34 | date = March 2005 | pmid = 15766526 | doi = 10.1016/j.cell.2004.12.038 | doi-access = free }}</ref> It has been demonstrated that given complete complementarity between the miRNA and target mRNA sequence, Ago2 can cleave the mRNA and lead to direct mRNA degradation. In the absence of complementarity, silencing is achieved by preventing translation.<ref name="pmid15685193"/> The relation of miRNA and its target mRNA can be based on the simple negative regulation of a target mRNA, but it seems that a common scenario is the use of a "coherent [[Feed forward (control)|feed-forward]] loop", "mutual negative feedback loop" (also termed double negative loop) and "positive feedback/feed-forward loop". Some miRNAs work as buffers of random gene expression changes arising due to stochastic events in transcription, translation and protein stability. Such regulation is typically achieved by the virtue of negative feedback loops or incoherent feed-forward loop uncoupling protein output from mRNA transcription.