ScholarlyCommons

Title

RNase-Mediated Protein Footprint Sequencing Reveals Protein-Binding Sites Throughout the Human Transcriptome

Author(s)

Ian M. Silverman, University of Pennsylvania
Fan Li, University of Pennsylvania
Anissa Alexander, University of Pennsylvania
Loyal Goff, Harvard University
Cole Trapnell, Harvard University
John L. Rinn, Harvard University
Brian D. Gregory, University of PennsylvaniaFollow

Document Type

Technical Report

Date of this Version

2014

Publication Source

Genome Biology

Volume

15

DOI

10.1186/gb-2014-15-1-r3

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.

Copyright/Permission Statement

© Silverman et al.; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Recommended Citation

Silverman, I. M., Li, F., Alexander, A., Goff, L., Trapnell, C., Rinn, J. L., & Gregory, B. D. (2014). RNase-Mediated Protein Footprint Sequencing Reveals Protein-Binding Sites Throughout the Human Transcriptome. Genome Biology, 15 http://dx.doi.org/10.1186/gb-2014-15-1-r3