HITS-CLIP: Difference between revisions

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'''High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation''' ('''HITS-CLIP''') is a [[genome]]-wide means of mapping [[protein]]&ndash;[[RNA]] binding sites [[in vivo]].<ref>Darnell RB (2010) HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley Interdiscip Rev RNA. 1) 266-86. {{DOI|10.1002/wrna.31}} PMID 21935890</ref><ref name="Licatalosi DD, Mele A, Fak JJ, et al. 2008 464–9">{{cite journal |author=Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB. |title=HITS-CLIP yields genome-wide insights into brain alternative RNA processing |journal=Nature |volume=456 |issue=7221 |pages=464–9 |date=November 2008 |pmid=18978773 |pmc=2597294 |doi=10.1038/nature07488}}</ref> HITS-CLIP was originally used to generate genome-wide protein-RNA interaction maps for the neuron-specific [[RNA-binding protein]] and [[splicing factor]] [[NOVA1]] and NOVA2;<ref name="Licatalosi DD, Mele A, Fak JJ, et al. 2008 464–9" /> since then a number of other splicing factor maps have been generated, including those for PTB,<ref>{{citation |journal=Molecular Cell |author=Xue Y, Zhou Y, Wu T, Zhu T, Ju X, Kwon YS, Zhang C, Yeo G, Black DL, Sun H, Fu XD, Zhang Y |title= Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping |volume=36 |issue=6 |pages=996–1006 |year=2009 |PMID=20064465 |doi=10.1016/j.molcel.2009.12.003}}</ref> RbFox2,<ref>{{cite journal |author= Yeo GW, Coufal NG, Liang TY, Peng GE, Fu XD, Gage FH |title= An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells |journal= Nat Struct Mol Biol |volume=16 |issue=2 |pages=130–137 |year=2009 |PMID= 19136955 |pmc= 2735254 |doi=10.1038/nsmb.1545}}</ref> SFRS1,<ref>{{cite journal |author=Sanford JR, Wang X, Mort M, Fanduyn N, Cooper DN, Mooney SD, Edenberg HJ, Liu Y |title=Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts |journal=Genome Research |volume=19 |issue=3 |pages=381–394 |year=2009 |PMID= 19116412 |pmc=2661799 |doi=10.1101/gr.082503.108}}</ref> and hnRNP C.<ref>{{citation |journal=Nat Struct Mol Biol |author=Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J |title=iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution |volume=17 |issue=7 |pages=909–915|year=2010 |PMID=20601959 |pmc=3000544 |doi=10.1038/nsmb.1838}}</ref>

HITS-CLIP of the RNA-binding protein [[Argonaute]] has been performed for the identification of microRNA targets<ref>{{cite journal|last=Thomson|first=DW|coauthors=Bracken, CP, 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}}</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 |author=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 |author=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 |author=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=21894221 |doi=10.1038/nsmb0911-1084a}}</ref> and tissue culture cells.<ref>{{citation |journal=Cell |author=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> 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>

==Similar methods==