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High-resolution profiling of protein occupancy on polyadenylated RNA transcripts

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Item Type:Article
Title:High-resolution profiling of protein occupancy on polyadenylated RNA transcripts
Creators Name:Munschauer, M. and Schueler, M. and Dieterich, C. and Landthaler, M.
Abstract:A key prerequisite to understand how gene regulatory processes are controlled by the interplay of RNA-binding proteins (RBPs) and ribonucleoprotein complexes with RNAs is the generation of comprehensive high-resolution maps of protein-RNA interactions. Recent advances in next-generation sequencing technology accelerated the development of various crosslinking and immunoprecipitation (CLIP) approaches to broadly identify RNA regions contacted by RNA-binding proteins. However these methods only consider single RNA-binding proteins and their contact sites, irrespective of the overall cis-regulatory sequence space contacted by other RNA interacting factors. Here we describe the application of protein occupancy profiling, a novel approach that globally displays the RNA contact sites of the poly(A)+ RNA-bound proteome. Protein occupancy profiling enables the generation of transcriptome-wide maps of protein-RNA interactions on polyadenylated transcripts and narrows the sequence search space for transcript regions involved in cis-regulation of gene expression in response to internal or external stimuli, altered cellular programs or disease.
Keywords:CLIP, PAR-CLIP, mRNA, lincRNA, Protein Occupancy Profiling, Non-Coding RNA, Protein-RNA Interaction, RNA-Binding Protein, Next-Generation Sequencing, Animals, Mice
Source:Methods
ISSN:1046-2023
Publisher:Elsevier (The Netherlands)
Volume:65
Number:3
Page Range:302-309
Date:February 2014
Official Publication:https://doi.org/10.1016/j.ymeth.2013.09.017
PubMed:View item in PubMed

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