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

Ian M. Silverman, Fan Li, Anissa Alexander, Loyal Goff, Cole Trapnell, John L. Rinn, Brian D. Gregory

Research output: Contribution to journalArticlepeer-review

53 Scopus citations

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.

Original languageEnglish (US)
Article numberR3
JournalGenome biology
Volume15
Issue number1
DOIs
StatePublished - Jan 7 2014
Externally publishedYes

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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