HITS-CLIP: Difference between revisions

Revision as of 22:52, 10 August 2016

Revision as of 22:52, 10 August 2016

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HITS-CLIP of the RNA-binding protein [[Argonaute]] has been performed for the identification of microRNA targets<ref>{{cite journal|last=Thomson|first=DW |author2=Bracken, CP |author3=Goodall, GJ|title=Experimental strategies for microRNA target identification.|journal=Nucleic Acids Research|date=2011-06-07|pmid=21652644|doi=10.1093/nar/gkr330|pmc=3167600|volume=39|issue=16|pages=6845–6853}}</ref> by decoding [[microRNA]]-mRNA and protein-RNA interaction maps in mouse brain,<ref name="Chi,S.W., Zang,J.B., Mele,A. and Darnell,R.B. 2009 479–486">{{citation |journal=Nature |author=Chi,S.W., Zang,J.B., Mele,A. and Darnell,R.B. |title=Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps |volume=460|issue=7254 |pages=479–486 |year=2009 |pmid=19536157 |pmc=2733940 |doi=10.1038/nature08170}}</ref><ref name="pmid21037263">{{cite journal |vauthors=Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH |title=starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. |journal=Nucl. Acids Res. |volume=39|issue=Database issue |pages=D202-D209 |year=2011 |pmid=21037263 |doi=10.1093/nar/gkq1056 |pmc=3013664}}</ref> and subsequently in ''[[Caenorhabditis elegans]]'',<ref>{{citation |journal=Nat Struct Mol Biol |vauthors=Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo GW |title=Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans |volume=17 |issue=2 |pages=173–179 |year=2010 |pmid=20062054 |pmc=2834287 |doi=10.1038/nsmb.1745}}</ref> [[embryonic stem cells]]<ref>{{citation |journal=Nat Struct Mol Biol |vauthors=Leung AK, Young AG, Bhutkar A, Zheng GX, Bosson AD, Nielsen CB, Sharp PA |title=Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs |volume=19 |issue=9 |pages=1084 |year=2011 |pmid=<!--none--> |doi=10.1038/nsmb0911-1084a}}</ref> and tissue culture cells.<ref>{{citation |journal=Cell |vauthors=Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, ((Ascano M Jr)), Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T |title=Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP |volume=141 |issue=1 |pages=129–141 |year=2010 |pmid=20371350 |pmc=2861495 |doi=10.1016/j.cell.2010.03.009}}</ref>

OneAs a novel modification of HITS-CLIP, m6A-CLIP has beenwas developed to precisely map m6A locations in mRNA by UV-crosslinking m6A antibody to the target RNA. <ref name="ke2015">{{cite journal|last1=Ke|first1=S|last2=Alemu|first2=EA|last3=Mertens|first3=C|last4=Gantman|first4=EC|last5=Fak|first5=JJ|last6=Mele|first6=A|last7=Haripal|first7=B|last8=Zucker-Scharff|first8=I|last9=Moore|first9=MJ|last10=Park|first10=CY|last11=Vågbø|first11=CB|last12=Kusnierczyk|first12=A|last13=Klungland|first13=A|last14=Darnell|first14=JE|last15=Darnell|first15=RB|title=A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation.|journal=Genes & Development|date=24 September 2015|volume=29|issue=19|pages=2037–53|pmid=26404942|doi=10.1101/gad.269415.115}}</ref>

Recently, improved [[bioinformatics]] applied to Argonaute HITS-CLIP enables identification of binding sites with single nucleotide resolution.<ref>{{cite journal |journal=Nature Biotechnology |author=Zhang,C. and Darnell,R.B. |title=Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. |volume=29 |issue=7 |pages=607–614 |year=2011 |pmid= 21633356 |doi=10.1038/nbt.1873 |pmc=3400429}}</ref>