Editing RNA (section)

=== Regulatory RNA ===

The earliest known regulators of [[gene expression]] were proteins known as [[repressor]]s and [[Activator (genetics)|activators]] – regulators with specific short binding sites within [[Enhancer (genetics)|enhancer]] regions near the genes to be regulated.<ref>{{cite journal | vauthors = Jacob F, Monod J | year = 1961 | title = Genetic Regulatory Mechanisms in the Synthesis of Proteins | journal = Journal of Molecular Biology | volume = 3 | issue = 3| pages = 318–56 | doi = 10.1016/s0022-2836(61)80072-7 | pmid = 13718526 | s2cid = 19804795 }}</ref>&nbsp; Later studies have shown that RNAs also regulate genes. There are several kinds of RNA-dependent processes in eukaryotes regulating the expression of genes at various points, such as [[RNA interference]] repressing genes [[Post-transcriptional regulation|post-transcriptionally]],  [[long non-coding RNA]]s shutting down blocks of [[chromatin]] [[epigenetically]], and [[enhancer RNA]]s inducing increased gene expression.<ref name="Morris-2014">{{cite journal | vauthors = Morris K, Mattick J | year = 2014 | title = The rise of regulatory RNA | journal = Nature Reviews Genetics | volume = 15 | issue = 6| pages = 423–37 | doi = 10.1038/nrg3722 | pmid = 24776770 | pmc = 4314111 }}</ref> [[Prokaryote|Bacteria and archaea]]  have also been shown to use regulatory RNA systems such as [[bacterial small RNA]]s and [[CRISPR]].<ref name="Gottesman-2005">{{cite journal | vauthors = Gottesman S | year = 2005 | title = Micros for microbes: non-coding regulatory RNAs in bacteria | journal = Trends in Genetics | volume = 21 | issue = 7| pages = 399–404 | doi = 10.1016/j.tig.2005.05.008 | pmid = 15913835 }}</ref>  Fire and Mello were awarded the 2006 [[Nobel Prize in Physiology or Medicine]] for discovering [[microRNA]]s  (miRNAs), specific short RNA molecules that can base-pair with mRNAs.<ref name="Nobel Prize-2006">"The Nobel Prize in Physiology or Medicine 2006". ''Nobelprize.org.'' Nobel Media AB 2014. Web. 6 Aug 2018. http://www.nobelprize.org/nobel_prizes/medicine/laureates/2006</ref>

==== MicroRNA (miRNA) and small interfering RNA (siRNA) ====
{{See also|RNA interference}}

Post-transcriptional expression levels of many genes can be controlled by [[RNA interference]], in which [[miRNA]]s, specific short RNA molecules, pair with mRNA regions and target them for degradation.<ref>{{cite journal | vauthors = Fire  | display-authors = etal | year = 1998 | title = Potent and Specific Genetic Interference by double stranded RNA in Ceanorhabditis elegans | journal = Nature | volume = 391 | issue = 6669| pages = 806–11 | doi = 10.1038/35888 | pmid = 9486653 | bibcode = 1998Natur.391..806F | s2cid = 4355692 | url = http://www.dspace.cam.ac.uk/handle/1810/238264 }}</ref>  This [[Antisense RNA|antisense]]-based process involves steps that first process the RNA so that it can [[Base pair|base-pair]] with a region of its target mRNAs. Once the base pairing occurs, other proteins direct the mRNA to be destroyed by [[nuclease]]s.<ref name="Morris-2014" />

==== Long non-coding RNAs ====
{{See also|Long non-coding RNA|l1=Long Non-coding RNA}}

Next to be linked to regulation were [[XIST|Xist]] and other [[long noncoding RNA]]s associated with [[X chromosome inactivation]].&nbsp; Their roles, at first mysterious, were shown by [[Jeannie T. Lee]] and others to be the [[RNA silencing|silencing]] of blocks of chromatin via recruitment of [[Polycomb-group proteins|Polycomb]] complex so that messenger RNA could not be transcribed from them.<ref>{{cite journal | vauthors = Zhao J, Sun BK, Erwin JA, Song JJ, Lee JT | year = 2008 | title = Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome | journal = Science | volume = 322 | issue = 5902| pages = 750–56 | pmid = 18974356 | doi = 10.1126/science.1163045 | pmc = 2748911 | bibcode = 2008Sci...322..750Z }}</ref> Additional lncRNAs, currently defined as RNAs of more than 200 base pairs that do not appear to have coding potential,<ref name="Rinn-2012">{{cite journal | vauthors = Rinn JL, Chang HY | year = 2012 | title = Genome regulation by long noncoding RNAs | journal = Annu. Rev. Biochem. | volume = 81 | pages = 1–25 | doi = 10.1146/annurev-biochem-051410-092902 | pmid = 22663078 | pmc = 3858397 }}</ref> have been found associated with regulation of [[stem cell]] [[pluripotency]] and [[cell division]].<ref name="Rinn-2012" />

==== Enhancer RNAs ====
{{See also|Enhancer RNA}}

The third major group of regulatory RNAs is called [[enhancer RNA]]s.<ref name="Rinn-2012" /> &nbsp;It is not clear at present whether they are a unique category of RNAs of various lengths or&nbsp;constitute a distinct subset of lncRNAs.&nbsp; In any case, they are transcribed from [[enhancers]], which are known regulatory sites in the DNA near genes they regulate.<ref name="Rinn-2012" /><ref>{{cite journal | vauthors = Taft RJ, Kaplan CD, Simons C, Mattick JS | year = 2009 | title = Evolution, biogenesis and function of promoter- associated RNAs | journal = Cell Cycle | volume = 8 | issue = 15| pages = 2332–38 | doi = 10.4161/cc.8.15.9154 | pmid = 19597344 | doi-access = free }}</ref> &nbsp;They up-regulate the transcription of the gene(s) under control of the enhancer from which they are transcribed.<ref name="Rinn-2012" /><ref>{{cite journal | vauthors = Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A | display-authors = etal | year = 2010 | title = 'Long noncoding RNAs with enhancer-like function in human cells | journal = Cell | volume = 143 | issue = 1| pages = 46–58 | pmid = 20887892 | doi = 10.1016/j.cell.2010.09.001 | pmc = 4108080 }}</ref>