HITS-CLIP

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] HITS-CLIP was originally used to generate genome-wide protein-RNA interaction maps for the neuron-specific RNA binding protein and splicing factor Nova;[1] since then a number of other splicing factor maps have been generated, including those for PTB,[2] RbFox2,[3] SFRS1,[4] and hnRNP C.[5]

HITS-CLIP of the RNA binding protein Argonaute has been performed for the identification of microRNA targets [6] by decoding microRNA-mRNA and protein-RNA interaction maps in mouse brain,[7][8] and subsequently in Caenorhabditis elegans,[9] embryonic stem cells[10] and tissue culture cells.[11] Recently, improved bioinformatics applied to Argonaute HITS-CLIP enables identification of binding sites with single nucleotide resolution.[12]

Similar methods

External links

References

  1. ^ 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. (November 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2597294. 
  2. ^ 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 
  3. ^ 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2735254. 
  4. ^ Sanford JR, Wang X, Mort M, Fanduyn N, Cooper DN, Mooney SD, Edenberg HJ, Liu Y (2009). Genome Research 19 (3): 381–394. doi:10.1101/gr.082503.108. PMC 2661799. PMID 19116412. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2661799. 
  5. ^ 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, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3000544 
  6. ^ Thomson, DW; Bracken, CP, Goodall, GJ (2011-06-07). "Experimental strategies for microRNA target identification.". Nucleic Acids Research. doi:10.1093/nar/gkr330. PMC 3167600. PMID 21652644. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3167600. 
  7. ^ 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, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2733940 
  8. ^ 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3013664. 
  9. ^ 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, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2834287 
  10. ^ 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 
  11. ^ 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, http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2861495 
  12. ^ 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.