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
- ↑ 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
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