Date of this Version
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.
© 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.
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
Additional FilesAdd File 1_RNase-mediated protein footprint sequencing.xlsx (43 kB)
Add File 2_RNase-mediated protein footprint sequencing.jpeg (1216 kB)
Add File 3_RNase-mediated protein footprint sequencing.jpeg (646 kB)
Add File 4_RNase-mediated protein footprint sequencing.jpeg (520 kB)
Add File 5_RNase-mediated protein footprint sequencing.jpeg (737 kB)
Add File 6_RNase-mediated protein footprint sequencing.jpeg (619 kB)
Add File 7_RNase-mediated protein footprint sequencing.jpeg (923 kB)
Add File 8_RNase-mediated protein footprint sequencing.jpeg (917 kB)
Add File 9_RNase-mediated protein footprint sequencing.jpeg (439 kB)
Add File 10_RNase-mediated protein footprint sequencing.xlsx (698 kB)
Add File 11_RNase-mediated protein footprint sequencing.xlsx (455 kB)
Date Posted: 14 July 2017
This document has been peer reviewed.