Literature DB >> 27765618

Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins.

Aitor Garzia1, Cindy Meyer1, Pavel Morozov1, Marcin Sajek1, Thomas Tuschl2.   

Abstract

Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in combination with next-generation sequencing is a powerful method for identifying endogenous targets of RNA-binding proteins (RBPs). Depending on the characteristics of each RBP, key steps in the PAR-CLIP procedure must be optimized. Here we present a comprehensive step-by-step PAR-CLIP protocol with detailed explanations of the critical steps. Furthermore, we report the application of a new PAR-CLIP data analysis pipeline to three distinct RBPs targeting different annotation categories of cellular RNAs.
Copyright © 2016 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Next-generation sequencing; Photocrosslinking; Ribonucleoprotein analysis; UV RNA-protein crosslinking

Mesh：

Substances：

Year:  2016        PMID： 27765618      PMCID： PMC5393971          DOI： 10.1016/j.ymeth.2016.10.007

Source DB:  PubMed          Journal:  Methods        ISSN： 1046-2023            Impact factor:   3.608


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