Editing MicroRNA (section)

==Biogenesis==
[[File:MiRNA-biogenesis.jpg|thumb|400px]]

As many as 40% of miRNA genes may lie in the [[intron]]s or even [[exon]]s of other genes.<ref name="Rodriguez_2004">{{cite journal | vauthors = Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A | title = Identification of mammalian microRNA host genes and transcription units | journal = Genome Research | volume = 14 | issue = 10A | pages = 1902–10 | date = October 2004 | pmid = 15364901 | pmc = 524413 | doi = 10.1101/gr.2722704 }}</ref> These are usually, though not exclusively, found in a sense orientation,<ref name="Cai_2004" /><ref name="pmid15634332">{{cite journal | vauthors = Weber MJ | title = New human and mouse microRNA genes found by homology search | journal = The FEBS Journal | volume = 272 | issue = 1 | pages = 59–73 | date = January 2005 | pmid = 15634332 | doi = 10.1111/j.1432-1033.2004.04389.x | s2cid = 32923462 | doi-access = free }}</ref> and thus usually are regulated together with their host genes.<ref name="Rodriguez_2004" /><ref name="pmid17255951">{{cite journal | vauthors = Kim YK, Kim VN | title = Processing of intronic microRNAs | journal = The EMBO Journal | volume = 26 | issue = 3 | pages = 775–83 | date = February 2007 | pmid = 17255951 | pmc = 1794378 | doi = 10.1038/sj.emboj.7601512 }}</ref><ref name="pmid15701730">{{cite journal | vauthors = Baskerville S, Bartel DP | title = Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes | journal = RNA | volume = 11 | issue = 3 | pages = 241–47 | date = March 2005 | pmid = 15701730 | pmc = 1370713 | doi = 10.1261/rna.7240905 }}</ref>

The DNA template is not the final word on mature miRNA production: 6% of human miRNAs show RNA editing ([[Isomir|IsomiRs]]), the site-specific modification of RNA sequences to yield products different from those encoded by their DNA. This increases the diversity and scope of miRNA action beyond that implicated from the genome alone.

===Transcription===
miRNA genes are usually transcribed by [[RNA polymerase II]] (Pol II).<ref name="LeeEMBO">{{cite journal | vauthors = Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN | title = MicroRNA genes are transcribed by RNA polymerase II | journal = The EMBO Journal | volume = 23 | issue = 20 | pages = 4051–60 | date = October 2004 | pmid = 15372072 | pmc = 524334 | doi = 10.1038/sj.emboj.7600385 }}</ref><ref name="Zhou_2007">{{cite journal | vauthors = Zhou X, Ruan J, Wang G, Zhang W | title = Characterization and identification of microRNA core promoters in four model species | journal = PLOS Computational Biology | volume = 3 | issue = 3 | pages = e37 | date = March 2007 | pmid = 17352530 | pmc = 1817659 | doi = 10.1371/journal.pcbi.0030037 | bibcode = 2007PLSCB...3...37Z | doi-access = free }}</ref> The polymerase often binds to a promoter found near the DNA sequence, encoding what will become the hairpin loop of the pre-miRNA. The resulting transcript is [[5' cap|capped]] with a specially modified nucleotide at the 5' end, [[Polyadenylation|polyadenylated]] with multiple [[Adenosine monophosphate|adenosines]] (a poly(A) tail),<ref name=LeeEMBO/><ref name="Cai_2004">{{cite journal | vauthors = Cai X, Hagedorn CH, Cullen BR | title = Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs | journal = RNA | volume = 10 | issue = 12 | pages = 1957–66 | date = December 2004 | pmid = 15525708 | pmc = 1370684 | doi = 10.1261/rna.7135204 }}</ref> and [[RNA splicing|spliced]]. Animal miRNAs are initially transcribed as part of one arm of an ~80 nucleotide RNA [[stem-loop|hairpin]] that in turn forms part of a several hundred nucleotide-long miRNA precursor termed a pri-miRNA.<ref name=LeeEMBO/><ref name="Cai_2004"/> When a hairpin precursor is found in the 3' UTR, a transcript may serve as a pri-miRNA and a mRNA.<ref name="Cai_2004"/> [[RNA polymerase III]] (Pol III) transcribes some miRNAs, especially those with upstream [[Alu sequence]]s, [[transfer RNA]]s (tRNAs), and [[mammalian wide interspersed repeat]] (MWIR) promoter units.<ref name="pmid18778799">{{cite journal | vauthors = Faller M, Guo F | title = MicroRNA biogenesis: there's more than one way to skin a cat | journal = Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms | volume = 1779 | issue = 11 | pages = 663–67 | date = November 2008 | pmid = 18778799 | pmc = 2633599 | doi = 10.1016/j.bbagrm.2008.08.005 }}</ref>

===Nuclear processing===
[[File:5b16 drosha dgcr8.png|thumb|right|A [[X-ray crystallography|crystal structure]] of the human [[Drosha]] protein in complex with the [[C-terminal]] [[alpha helix|helices]] of two [[DGCR8]] molecules (green). Drosha consists of two [[ribonuclease III]] domains (blue and orange); a double-stranded RNA binding domain (yellow); and a connector/platform domain (gray) containing two bound [[zinc]] ion (spheres). From {{PDB|5B16}}.]]

A single pri-miRNA may contain from one to six miRNA precursors. These hairpin loop structures are composed of about 70 nucleotides each. Each hairpin is flanked by sequences necessary for efficient processing.

The double-stranded RNA (dsRNA) structure of the hairpins in a pri-miRNA is recognized by a nuclear protein known as [[Pasha (protein)|DiGeorge Syndrome Critical Region 8]] (DGCR8 or "Pasha" in [[invertebrates]]), named for its association with [[DiGeorge Syndrome]]. DGCR8 associates with the enzyme [[Drosha]], a protein that cuts RNA, to form the [[Microprocessor complex]].<ref>{{cite journal | vauthors = Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Rådmark O, Kim S, Kim VN | title = The nuclear RNase III Drosha initiates microRNA processing | journal = Nature | volume = 425 | issue = 6956 | pages = 415–19 | date = September 2003 | pmid = 14508493 | doi = 10.1038/nature01957 | bibcode = 2003Natur.425..415L | s2cid = 4421030 }}</ref><ref name="pmid16957365">{{Cite book | vauthors = Gregory RI, Chendrimada TP, Shiekhattar R | title = MicroRNA Protocols | chapter = MicroRNA biogenesis: isolation and characterization of the microprocessor complex | series = Methods in Molecular Biology | volume = 342 | pages = 33–47 | year = 2006 | pmid = 16957365 | doi = 10.1385/1-59745-123-1:33 | isbn = 978-1-59745-123-9 }}</ref> In this complex, DGCR8 orients the catalytic RNase III domain of Drosha to liberate hairpins from pri-miRNAs by cleaving RNA about eleven nucleotides from the hairpin base (one helical dsRNA turn into the stem).<ref>{{cite journal | vauthors = Han J, Lee Y, Yeom KH, Kim YK, Jin H, Kim VN | title = The Drosha-DGCR8 complex in primary microRNA processing | journal = Genes & Development | volume = 18 | issue = 24 | pages = 3016–27 | date = December 2004 | pmid = 15574589 | pmc = 535913 | doi = 10.1101/gad.1262504 }}</ref><ref>{{cite journal | vauthors = Han J, Lee Y, Yeom KH, Nam JW, Heo I, Rhee JK, Sohn SY, Cho Y, Zhang BT, Kim VN | title = Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex | journal = Cell | volume = 125 | issue = 5 | pages = 887–901 | date = June 2006 | pmid = 16751099 | doi = 10.1016/j.cell.2006.03.043 | doi-access = free }}</ref> The product resulting has a two-nucleotide overhang at its 3' end; it has 3' hydroxyl and 5' phosphate groups. It is often termed as a pre-miRNA (precursor-miRNA). Sequence motifs downstream of the pre-miRNA that are important for efficient processing have been identified.<ref>{{cite journal | vauthors = Conrad T, Marsico A, Gehre M, Orom UA | title = Microprocessor activity controls differential miRNA biogenesis in Vivo | journal = Cell Reports | volume = 9 | issue = 2 | pages = 542–54 | date = October 2014 | pmid = 25310978 | doi = 10.1016/j.celrep.2014.09.007 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Auyeung VC, Ulitsky I, McGeary SE, Bartel DP | title = Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing | journal = Cell | volume = 152 | issue = 4 | pages = 844–58 | date = February 2013 | pmid = 23415231 | pmc = 3707628 | doi = 10.1016/j.cell.2013.01.031 }}</ref><ref name="ali">{{cite journal | vauthors = Ali PS, Ghoshdastider U, Hoffmann J, Brutschy B, Filipek S | title = Recognition of the let-7g miRNA precursor by human Lin28B | journal = FEBS Letters | volume = 586 | issue = 22 | pages = 3986–90 | date = November 2012 | pmid = 23063642 | doi = 10.1016/j.febslet.2012.09.034 | s2cid = 28899778 | doi-access = free | bibcode = 2012FEBSL.586.3986S }}</ref>

Pre-miRNAs that are [[RNA splicing|spliced]] directly out of introns, bypassing the Microprocessor complex, are known as "[[mirtrons]]."<ref name="Intronic microRNA precursors that b">{{cite journal | vauthors = Ruby JG, Jan CH, Bartel DP | title = Intronic microRNA precursors that bypass Drosha processing | journal = Nature | volume = 448 | issue = 7149 | pages = 83–86 | date = July 2007 | pmid = 17589500 | pmc = 2475599 | doi = 10.1038/nature05983 | bibcode = 2007Natur.448...83R }}</ref> Mirtrons have been found in ''Drosophila'', ''C. elegans'', and mammals.<ref name="Intronic microRNA precursors that b"/><ref name="pmid17964270">{{cite journal | vauthors = Berezikov E, Chung WJ, Willis J, Cuppen E, Lai EC | title = Mammalian mirtron genes | journal = Molecular Cell | volume = 28 | issue = 2 | pages = 328–336 | date = October 2007 | pmid = 17964270 | pmc = 2763384 | doi = 10.1016/j.molcel.2007.09.028 }}</ref>

As many as 16% of pre-miRNAs may be altered through nuclear [[RNA editing]].<ref name="pmid18684997">{{cite journal | vauthors = Kawahara Y, Megraw M, Kreider E, Iizasa H, Valente L, Hatzigeorgiou AG, Nishikura K | title = Frequency and fate of microRNA editing in human brain | journal = Nucleic Acids Research | volume = 36 | issue = 16 | pages = 5270–80 | date = September 2008 | pmid = 18684997 | pmc = 2532740 | doi = 10.1093/nar/gkn479 }}</ref><ref name="pmid19255566">{{cite journal | vauthors = Winter J, Jung S, Keller S, Gregory RI, Diederichs S | title = Many roads to maturity: microRNA biogenesis pathways and their regulation | journal = Nature Cell Biology | volume = 11 | issue = 3 | pages = 228–34 | date = March 2009 | pmid = 19255566 | doi = 10.1038/ncb0309-228 | s2cid = 205286318 }}</ref><ref name="pmid17628290">{{cite journal | vauthors = Ohman M | title = A-to-I editing challenger or ally to the microRNA process | journal = Biochimie | volume = 89 | issue = 10 | pages = 1171–76 | date = October 2007 | pmid = 17628290 | doi = 10.1016/j.biochi.2007.06.002 }}</ref> Most commonly, [[enzyme]]s known as [[adenosine deaminase]]s acting on RNA (ADARs) catalyze [[adenosine]] to [[inosine]] (A to I) transitions. RNA editing can halt nuclear processing (for example, of pri-miR-142, leading to degradation by the ribonuclease Tudor-SN) and alter downstream processes including cytoplasmic miRNA processing and target specificity (e.g., by changing the seed region of miR-376 in the central nervous system).<ref name="pmid18684997" />

===Nuclear export===
[[File:3a6p xpo5 ran miRNA.png|thumb|left|The human exportin-5 protein (red) in complex with [[Ran-GTP]] (yellow) and a pre-microRNA (green), showing two-[[nucleotide]] overhang recognition element (orange). From {{PDB|3A6P}}.]]

Pre-miRNA hairpins are exported from the nucleus in a process involving the nucleocytoplasmic shuttler [[XPO5|Exportin-5]]. This protein, a member of the [[karyopherin|karyopherin family]], recognizes a two-nucleotide overhang left by the RNase III enzyme Drosha at the 3' end of the pre-miRNA hairpin. Exportin-5-mediated transport to the cytoplasm is energy-dependent, using [[guanosine triphosphate]] (GTP) bound to the [[Ran (biology)|Ran]] protein.<ref name="pmid15145345">{{cite journal | vauthors = Murchison EP, Hannon GJ | title = miRNAs on the move: miRNA biogenesis and the RNAi machinery | journal = Current Opinion in Cell Biology | volume = 16 | issue = 3 | pages = 223–29 | date = June 2004 | pmid = 15145345 | doi = 10.1016/j.ceb.2004.04.003 | author-link2 = Gregory Hannon | author-link1 = Elizabeth Murchison }} {{closed access}}</ref>

===Cytoplasmic processing===
In the [[cytoplasm]], the pre-miRNA hairpin is cleaved by the RNase III enzyme [[Dicer]].<ref name="pmid17381281">{{cite journal | vauthors = Lund E, Dahlberg JE | title = Substrate selectivity of exportin 5 and Dicer in the biogenesis of microRNAs | journal = Cold Spring Harbor Symposia on Quantitative Biology | volume = 71 | pages = 59–66 | year = 2006 | pmid = 17381281 | doi = 10.1101/sqb.2006.71.050 | doi-access = free }}</ref> This endoribonuclease interacts with 5' and 3' ends of the hairpin<ref>{{cite journal | vauthors = Park JE, Heo I, Tian Y, Simanshu DK, Chang H, Jee D, Patel DJ, Kim VN | title = Dicer recognizes the 5' end of RNA for efficient and accurate processing | journal = Nature | volume = 475 | issue = 7355 | pages = 201–05 | date = July 2011 | pmid = 21753850 | pmc = 4693635 | doi = 10.1038/nature10198 }}</ref> and cuts away the loop joining the 3' and 5' arms, yielding an imperfect miRNA:miRNA* duplex about 22 nucleotides in length.<ref name=pmid17381281/> Overall hairpin length and loop size influence the efficiency of Dicer processing. The imperfect nature of the miRNA:miRNA* pairing also affects cleavage.<ref name=pmid17381281/><ref name="pmid18268841">{{Cite book | vauthors = Ji X | chapter = The Mechanism of RNase III Action: How Dicer Dices | volume = 320 | pages = 99–116 | year = 2008 | pmid = 18268841 | doi = 10.1007/978-3-540-75157-1_5 | isbn = 978-3-540-75156-4 | series = Current Topics in Microbiology and Immunology | title = RNA Interference }}</ref> Some of the G-rich pre-miRNAs can potentially adopt the [[G-quadruplex]] structure as an alternative to the canonical hairpin structure. For example, human pre-miRNA 92b adopts a [[G-quadruplex]] structure which is resistant to the Dicer mediated cleavage in the [[cytoplasm]].<ref>{{cite journal | vauthors = Mirihana Arachchilage G, Dassanayake AC, Basu S | title = A potassium ion-dependent RNA structural switch regulates human pre-miRNA 92b maturation | journal = Chemistry & Biology | volume = 22 | issue = 2 | pages = 262–72 | date = February 2015 | pmid = 25641166 | doi = 10.1016/j.chembiol.2014.12.013 | doi-access = free }}</ref> Although either strand of the duplex may potentially act as a functional miRNA, only one strand is usually incorporated into the [[RNA-induced silencing complex]] (RISC) where the miRNA and its mRNA target interact.

While the majority of miRNAs are located within the cell, some miRNAs, commonly known as circulating miRNAs or extracellular miRNAs, have also been found in extracellular environment, including various biological fluids and cell culture media.<ref>{{cite journal | doi = 10.1016/j.als.2016.11.007 | volume=10 | issue=2 | title=Extracellular/Circulating MicroRNAs: Release Mechanisms, Functions and Challenges | journal=Achievements in the Life Sciences | pages=175–186| year=2016 | vauthors = Sohel MH | doi-access=free }}</ref><ref name="Boeckel 616–617">{{cite journal | vauthors = Boeckel JN, Reis SM, Leistner D, Thomé CE, Zeiher AM, Fichtlscherer S, Keller T | title = From heart to toe: heart's contribution on peripheral microRNA levels | journal = International Journal of Cardiology | volume = 172 | issue = 3 | pages = 616–17 | date = April 2014 | pmid = 24508494 | doi = 10.1016/j.ijcard.2014.01.082 }}</ref>

===Biogenesis in plants===
miRNA biogenesis in plants differs from [[abiogenesis|animal biogenesis]] mainly in the steps of nuclear processing and export. Instead of being cleaved by two different enzymes, once inside and once outside the nucleus, both cleavages of the plant miRNA are performed by a Dicer homolog, called [[Dicer-like1]] (DL1). DL1 is expressed only in the nucleus of plant cells, which indicates that both reactions take place inside the nucleus. Before plant miRNA:miRNA* duplexes are transported out of the nucleus, its 3' overhangs are methylated by a [[Methyltransferase|RNA methyltransferaseprotein]] called [[Hua-Enhancer1]] (HEN1). The duplex is then transported out of the nucleus to the cytoplasm by a protein called Hasty (HST), an Exportin 5 homolog, where they disassemble and the mature miRNA is incorporated into the RISC.<ref name="pmid20808519">{{cite journal | vauthors = Lelandais-Brière C, Sorin C, Declerck M, Benslimane A, Crespi M, Hartmann C | title = Small RNA diversity in plants and its impact in development | journal = Current Genomics | volume = 11 | issue = 1 | pages = 14–23 | date = March 2010 | pmid = 20808519 | pmc = 2851111 | doi = 10.2174/138920210790217918 }}</ref>