Skip to content

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

52Citations
Citations of this article
215Readers
Mendeley users who have this article in their library.

This artice is free to access.

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

Cite

CITATION STYLE

APA

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(1). https://doi.org/10.1186/gb-2014-15-1-r3

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free