Silverman, Ian MLi, FanAlexander, AnissaGoff, LoyalTrapnell, ColeRinn, John LGregory, Brian D2023-05-222023-05-222014-01-012017-07-11https://repository.upenn.edu/handle/20.500.14332/5518Although 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.© 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.Amino Acids, Peptides, and ProteinsBiologyCell BiologyGenomicsReport