Silverman, Ian MLi, FanAlexander, AnissaGoff, LoyalTrapnell, ColeRinn, JohnGregory, Brian D2014-07-072014Silverman, Ian M, Fan Li, Anissa Alexander, Loyal Goff, Cole Trapnell, John L Rinn, and Brian D Gregory. 2014. “RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome.” Genome Biology 15 (1): R3. doi:10.1186/gb-2014-15-1-r3. http://dx.doi.org/10.1186/gb-2014-15-1-r3.1465-6906http://nrs.harvard.edu/urn-3:HUL.InstRepos:12406527Although 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.en-USJournal Article2014-07-0710.1186/gb-2014-15-1-r3