RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

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RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome

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Title: RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome
Author: Silverman, Ian M; Li, Fan; Alexander, Anissa; Goff, Loyal; Trapnell, Cole; Rinn, John L; Gregory, Brian D

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Citation: Silverman, 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.
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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.
Published Version: doi:10.1186/gb-2014-15-1-r3
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053792/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:12406527
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