HITS-CLIP: Difference between revisions

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'''High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation''' ('''HITS-CLIP''') is a variant of [[Cross-linking immunoprecipitation|CLIP]]<ref>{{Cite journal |lastlast1=Ule |firstfirst1=Jernej |last2=Jensen |first2=Kirk B. |last3=Ruggiu |first3=Matteo |last4=Mele |first4=Aldo |last5=Ule |first5=Aljaz |last6=Darnell |first6=Robert B. |date=2003-11-14 |title=CLIP identifies Nova-regulated RNA networks in the brain |url=https://pubmed.ncbi.nlm.nih.gov/14615540 |journal=Science (New York, N.Y.) |volume=302 |issue=5648 |pages=1212–1215 |doi=10.1126/science.1090095 |issn=1095-9203 |pmid=14615540|bibcode=2003Sci...302.1212U |s2cid=23420615 }}</ref> for [[genome]]-wide mapping [[protein]]&ndash;[[RNA]] binding sites or RNA modification sites [[in vivo]].<ref>{{cite journal | author = Darnell RB | year = 2010 | title = HITS-CLIP: panoramic views of protein-RNA regulation in living cells | journal = Wiley Interdiscip Rev RNA | volume = 1 | issue = 2| pages = 266–86 | doi = 10.1002/wrna.31 | pmid = 21935890 | pmc=3222227}}</ref><ref name="Licatalosi DD, Mele A, Fak JJ, et al. 2008 464–9">{{cite journal |vauthors=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|bibcode=2008Natur.456..464L }}</ref><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|pmc=4604345}}</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 |vauthors=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 |pmc=2807993}}</ref> RbFox2,<ref>{{cite journal |vauthors=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 |vauthors=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> hnRNP C,<ref>{{citation |journal=Nat Struct Mol Biol |vauthors=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> and even [[N6-Methyladenosine]] (m6A) mRNA modifications.<ref name="ke2015"/><ref name="ke2017">{{cite journal|last1=Ke|first1=S|last2=Pandya-Jones|first2=A|last3=Saito|first3=Y|last4=Fak|first4=JJ|last5=Vågbø|first5=CB|last6=Geula|first6=S|last7=Hanna|first7=JH|last8=Black|first8=DL|last9=Darnell|first9=JE|last10=Darnell|first10=RB|title=m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover.|journal=Genes & Development|date=15 May 2017|volume=31|issue=10|pages=990–1006|pmid=28637692|doi=10.1101/gad.301036.117|pmc=5495127}}</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 |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.|author2= Zang, J.B.|author3=Mele, A.|author4=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|bibcode=2009Natur.460..479C }}</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=Nucleic 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|pmc=3078052 }}</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>

As a novel modification of HITS-CLIP, m6A-CLIP was developed to precisely map N6-Methyladenosine(m6A) locations in mRNA by UV-crosslinking m6A antibody to the target RNA.<ref name="ke2015"/><ref name="ke2017"/> 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. |author2=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==

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== External links ==

* [http://cm.jefferson.edu/CLIPSim-MC/ CLIPSim-MC]: CLIPSim-MC is a tool that uses CLIP-seq data to find [[miRNA]]/MRE pairings using a Monte-Carlo-based approach.<ref>{{citation |journal=Scientific Reports |author1=Peter M. Clark |author2=Phillipe Loher |author3=Kevin Quann |author4=Jonathan Brody |author5=Eric R. Londin |author6=Isidore Rigoutsos |title=Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types |volume=4 |issue=5947 |pages=5947 |year=2014 |pmid=25103560 |doi=10.1038/srep05947 |pmc=4894423|bibcode=2014NatSR...4.5947C }}</ref>

* [https://web.archive.org/web/20110222111721/http://starbase.sysu.edu.cn/ starBase database]: a database for exploring miRNA-mRNA, miRNA-[[lncRNA]], miRNA-[[sncRNA]], miRNA-[[circRNA]], miRNA-[[pseudogene]], protein-[[lncRNA]], '''[[protein-RNA]]''' interactions and [[ceRNA]] networks from '''HITS-CLIP''' ('''[[CLIP-Seq]]''', '''PAR-CLIP''', '''[[iCLIP]]''', '''CLASH''') data, and '''[http://www.targetscan.org TargetScan]'''<ref>{{Cite journal|title = Predicting effective microRNA target sites in mammalian mRNAs|url = http://elifesciences.org/content/4/e05005|journal = eLife|date = 2015-08-12|issn = 2050-084X|pmc = 4532895|pmid = 26267216|pagesarticle-number = e05005|volume = 4|doi = 10.7554/eLife.05005|language = en|firstfirst1 = Vikram|lastlast1 = Agarwal|first2 = George W.|last2 = Bell|first3 = Jin-Wu|last3 = Nam|first4 = David P.|last4 = Bartel | doi-access=free }}</ref>''', PicTar, RNA22, miRanda and PITA''' microRNA target sites.

* [http://www.clipz.unibas.ch/ clipz]: a pipeline to analyze short RNA reads from HITS-CLIP experiments.

* [http://qbrc.swmed.edu/software/ dCLIP]: dCLIP is a Perl program for discovering differential binding regions in two comparative CLIP-Seq (HITS-CLIP, PAR-CLIP or iCLIP) experiments.