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Genome Biol. 2014 Jan 7;15(1):R3. doi: 10.1186/gb-2014-15-1-r3.

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome.

Abstract

Although numerous approaches have been developed to map RNA-binding sites of individual RNA-binding proteins (RBPs), few methods exist that allow assessment of global RBP-RNA interactions. Here, we describe PIP-seq, a universal, high-throughput, ribonuclease-mediated protein footprint sequencing approach that reveals RNA-protein interaction sites throughout a transcriptome of interest. We apply PIP-seq to the HeLa transcriptome and compare binding sites found using different cross-linkers and ribonucleases. From this analysis, we identify numerous putative RBP-binding motifs, reveal novel insights into co-binding by RBPs, and uncover a significant enrichment for disease-associated polymorphisms within RBP interaction sites.

PMID:
24393486
PMCID:
PMC4053792
DOI:
10.1186/gb-2014-15-1-r3
[Indexed for MEDLINE]
Free PMC Article

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