Wikipedia

HITS-CLIP

(Redirected fromCLIP-Seq)

High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation(HITS-CLIP) is a variant ofCLIP[1]forgenome-wide mappingprotein–RNAbinding sites or RNA modification sitesin vivo.[2][3][4]HITS-CLIP was originally used to generate genome-wide protein-RNA interaction maps for the neuron-specificRNA-binding proteinandsplicing factorNOVA1and NOVA2;[3]since then a number of other splicing factor maps have been generated, including those for PTB,[5]RbFox2,[6]SFRS1,[7]hnRNP C,[8]and evenN6-Methyladenosine(m6A) mRNA modifications.[4][9]

HITS-CLIP of the RNA-binding proteinArgonautehas been performed for the identification of microRNA targets[10]by decodingmicroRNA-mRNA and protein-RNA interaction maps in mouse brain,[11][12]and subsequently inCaenorhabditis elegans,[13]embryonic stem cells[14]and tissue culture cells.[15]

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.[4][9]Recently, improvedbioinformaticsapplied to Argonaute HITS-CLIP enables identification of binding sites with single nucleotide resolution.[16]

Similar methods

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  • PAR-CLIP,for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) in tissue culture cells.
  • iCLIP,for a thorough amplification of the cDNA library, including truncated cDNAs, thus also enabling an additional means to identify crosslink sites.

References

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  1. ^Ule, Jernej; Jensen, Kirk B.; Ruggiu, Matteo; Mele, Aldo; Ule, Aljaz; Darnell, Robert B. (2003-11-14)."CLIP identifies Nova-regulated RNA networks in the brain".Science.302(5648): 1212–1215.Bibcode:2003Sci...302.1212U.doi:10.1126/science.1090095.ISSN1095-9203.PMID14615540.S2CID23420615.
  2. ^Darnell RB (2010)."HITS-CLIP: panoramic views of protein-RNA regulation in living cells".Wiley Interdiscip Rev RNA.1(2): 266–86.doi:10.1002/wrna.31.PMC3222227.PMID21935890.
  3. ^abLicatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB (November 2008)."HITS-CLIP yields genome-wide insights into brain alternative RNA processing".Nature.456(7221): 464–9.Bibcode:2008Natur.456..464L.doi:10.1038/nature07488.PMC2597294.PMID18978773.
  4. ^abcKe, S; Alemu, EA; Mertens, C; Gantman, EC; Fak, JJ; Mele, A; Haripal, B; Zucker-Scharff, I; Moore, MJ; Park, CY; Vågbø, CB; Kusnierczyk, A; Klungland, A; Darnell, JE; Darnell, RB (24 September 2015)."A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation".Genes & Development.29(19): 2037–53.doi:10.1101/gad.269415.115.PMC4604345.PMID26404942.
  5. ^Xue Y, Zhou Y, Wu T, Zhu T, Ju X, Kwon YS, Zhang C, Yeo G, Black DL, Sun H, Fu XD, Zhang Y (2009), "Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping",Molecular Cell,36(6): 996–1006,doi:10.1016/j.molcel.2009.12.003,PMC2807993,PMID20064465
  6. ^Yeo GW, Coufal NG, Liang TY, Peng GE, Fu XD, Gage FH (2009)."An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells".Nat Struct Mol Biol.16(2): 130–137.doi:10.1038/nsmb.1545.PMC2735254.PMID19136955.
  7. ^Sanford JR, Wang X, Mort M, Fanduyn N, Cooper DN, Mooney SD, Edenberg HJ, Liu Y (2009)."Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts".Genome Research.19(3): 381–394.doi:10.1101/gr.082503.108.PMC2661799.PMID19116412.
  8. ^Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J (2010), "iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution",Nat Struct Mol Biol,17(7): 909–915,doi:10.1038/nsmb.1838,PMC3000544,PMID20601959
  9. ^abKe, S; Pandya-Jones, A; Saito, Y; Fak, JJ; Vågbø, CB; Geula, S; Hanna, JH; Black, DL; Darnell, JE; Darnell, RB (15 May 2017)."m6A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover".Genes & Development.31(10): 990–1006.doi:10.1101/gad.301036.117.PMC5495127.PMID28637692.
  10. ^Thomson, DW; Bracken, CP; Goodall, GJ (2011-06-07)."Experimental strategies for microRNA target identification".Nucleic Acids Research.39(16): 6845–6853.doi:10.1093/nar/gkr330.PMC3167600.PMID21652644.
  11. ^Chi, S.W.; Zang, J.B.; Mele, A.; Darnell, R.B. (2009), "Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps",Nature,460(7254): 479–486,Bibcode:2009Natur.460..479C,doi:10.1038/nature08170,PMC2733940,PMID19536157
  12. ^Yang JH, Li JH, Shao P, Zhou H, Chen YQ, Qu LH (2011)."starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data".Nucleic Acids Res.39(Database issue): D202–D209.doi:10.1093/nar/gkq1056.PMC3013664.PMID21037263.
  13. ^Zisoulis DG, Lovci MT, Wilbert ML, Hutt KR, Liang TY, Pasquinelli AE, Yeo GW (2010), "Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans",Nat Struct Mol Biol,17(2): 173–179,doi:10.1038/nsmb.1745,PMC2834287,PMID20062054
  14. ^Leung AK, Young AG, Bhutkar A, Zheng GX, Bosson AD, Nielsen CB, Sharp PA (2011), "Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs",Nat Struct Mol Biol,19(9): 1084,doi:10.1038/nsmb0911-1084a,PMC3078052
  15. ^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 (2010), "Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP",Cell,141(1): 129–141,doi:10.1016/j.cell.2010.03.009,PMC2861495,PMID20371350
  16. ^Zhang, C.; Darnell, R.B. (2011)."Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data".Nature Biotechnology.29(7): 607–614.doi:10.1038/nbt.1873.PMC3400429.PMID21633356.
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  • CLIPSim-MC:CLIPSim-MC is a tool that uses CLIP-seq data to findmiRNA/MRE pairings using a Monte-Carlo-based approach.[1]
  • starBase database:a database for exploring miRNA-mRNA, miRNA-lncRNA,miRNA-sncRNA,miRNA-circRNA,miRNA-pseudogene,protein-lncRNA,protein-RNAinteractions andceRNAnetworks fromHITS-CLIP(CLIP-Seq,PAR-CLIP,iCLIP,CLASH) data, andTargetScan[2],PicTar, RNA22, miRanda and PITAmicroRNA target sites.
  • clipz:a pipeline to analyze short RNA reads from HITS-CLIP experiments.
  • dCLIP:dCLIP is a Perl program for discovering differential binding regions in two comparative CLIP-Seq (HITS-CLIP, PAR-CLIP or iCLIP) experiments.
  1. ^Peter M. Clark; Phillipe Loher; Kevin Quann; Jonathan Brody; Eric R. Londin; Isidore Rigoutsos (2014), "Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types",Scientific Reports,4(5947): 5947,Bibcode:2014NatSR...4E5947C,doi:10.1038/srep05947,PMC4894423,PMID25103560
  2. ^Agarwal, Vikram; Bell, George W.; Nam, Jin-Wu; Bartel, David P. (2015-08-12)."Predicting effective microRNA target sites in mammalian mRNAs".eLife.4:e05005.doi:10.7554/eLife.05005.ISSN2050-084X.PMC4532895.PMID26267216.
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