This article is part of a special issue on RBPome.
RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome
- Equal contributors
1 Department of Biology, University of Pennsylvania, 433 S. University Ave, Philadelphia, PA 19104, USA
2 PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
3 Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
4 Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
5 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
6 Broad Institute, Cambridge, MA 02142, USA
7 Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
Genome Biology 2014, 15:R3 doi:10.1186/gb-2014-15-1-r3Published: 7 January 2014
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.