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HITS-CLIP

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High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) is a genome-wide means of mapping protein–RNA binding sites in vivo.[1][2] 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;[2] since then a number of other splicing factor maps have been generated, including those for PTB,[3] RbFox2,[4] SFRS1,[5] and hnRNP C.[6]

HITS-CLIP of the RNA-binding protein Argonaute has been performed for the identification of microRNA targets[7] by decoding microRNA-mRNA and protein-RNA interaction maps in mouse brain,[8][9] and subsequently in Caenorhabditis elegans,[10] embryonic stem cells[11] and tissue culture cells.[12] Recently, improved bioinformatics applied to Argonaute HITS-CLIP enables identification of binding sites with single nucleotide resolution.[13]

Similar methods

  • PAR-CLIP, for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) in tissue culture cells.
  • CLIP-Seq, a synonym for HITS-CLIP.

References

  1. ^ 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
  2. ^ a b Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB. (2008). "HITS-CLIP yields genome-wide insights into brain alternative RNA processing". Nature. 456 (7221): 464–9. doi:10.1038/nature07488. PMC 2597294. PMID 18978773. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  3. ^ 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, PMID 20064465{{citation}}: CS1 maint: multiple names: authors list (link)
  4. ^ 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. PMC 2735254. PMID 19136955.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  5. ^ 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. PMC 2661799. PMID 19116412.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  6. ^ 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, PMC 3000544, PMID 20601959{{citation}}: CS1 maint: multiple names: authors list (link)
  7. ^ Thomson, DW (2011-06-07). "Experimental strategies for microRNA target identification". Nucleic Acids Research. doi:10.1093/nar/gkr330. PMC 3167600. PMID 21652644. {{cite journal}}: Unknown parameter |coauthors= ignored (|author= suggested) (help)
  8. ^ Chi,S.W., Zang,J.B., Mele,A. and Darnell,R.B. (2009), "Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps", Nature, 460 (7254): 479–486, doi:10.1038/nature08170, PMC 2733940, PMID 19536157{{citation}}: CS1 maint: multiple names: authors list (link)
  9. ^ 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". Nucl. Acids Res. 39 (Database issue): D202 – D209. doi:10.1093/nar/gkq1056. PMC 3013664. PMID 21037263.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  10. ^ 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, PMC 2834287, PMID 20062054{{citation}}: CS1 maint: multiple names: authors list (link)
  11. ^ 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, PMID 21894221{{citation}}: CS1 maint: multiple names: authors list (link)
  12. ^ 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, PMC 2861495, PMID 20371350{{citation}}: CS1 maint: multiple names: authors list (link)
  13. ^ Zhang,C. and 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. PMID 21633356.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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