Editing MicroRNA (section)

===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" />