HITS-CLIP/CLIP-Seq/PTB-Seq

HITS-CLIP/CLIP-Seq/PTB-Seq RNA

High-throughput sequencing of CLIP cDNA library (HITS-CLIP ), crosslinking and immunoprecipitation sequencing (CLIP-Seq ) or polypyrimidine tract binding protein-sequencing (PTB-Seq ) map protein-RNA binding sites in vivo. This approach is similar to RIP-Seq, but uses crosslinking to stabilize the protein-RNA complexes. In this method, RNA-protein complexes are UV crosslinked and immunoprecipitated. The protein-RNA complexes are treated with RNase followed by Proteinase K. RNA is extracted and reverse-transcribed to cDNA. Deep sequencing of cDNA provides single-base resolution mapping of protein binding to RNAs.

• HITS-CLIP: Chi SW, Zang JB, Mele A, Darnell RB; (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460: 479-86
• CLIP-Seq: Johnson D. S., Mortazavi A., Myers R. M. and Wold B. (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502
• PTB-Seq: Xue Y., Zhou Y., Wu T., Zhu T., Ji X., et al. (2009) Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Mol Cell 36: 996-1006

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