title: RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome.
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.
authors.forename: Ian M
authors.initials: IM
authors.lastname: Silverman
authors.forename: Fan
authors.initials: F
authors.lastname: Li
authors.forename: Anissa
authors.initials: A
authors.lastname: Alexander
authors.forename: Loyal
authors.initials: L
authors.lastname: Goff
authors.forename: Cole
authors.initials: C
authors.lastname: Trapnell
authors.forename: John L
authors.initials: JL
authors.lastname: Rinn
authors.forename: Brian D
authors.initials: BD
authors.lastname: Gregory
mesh_terms: D001665:Binding Sites; D056726:Genetic Association Studies; D006367:HeLa Cells; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D023302:Protein Footprinting / Q000379:methods*; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D012260:Ribonucleases / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D016601:RNA-Binding Proteins; D012260:Ribonucleases