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][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.

External links

• CLIPSim-MC: CLIPSim-MC is a tool that uses CLIP-seq data to find miRNA/MRE pairings using a Monte-Carlo-based approach.^[14]
• 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 TargetScan^[15], PicTar, RNA22, miRanda and PITA microRNA 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.

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 PMID 21935890
2. 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.
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, PMC 2807993, PMID 20064465
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.
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.
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
7. 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. PMC 3167600. PMID 21652644.
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
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.
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
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
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
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. PMC 3400429. PMID 21633356.
14. 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), doi:10.1038/srep05947, PMID 25103560
15. 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. ISSN 2050-084X. PMC 4532895. PMID 26267216.