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

被引：39

作者：

Garzia, Aitor ^{[1
]}

Meyer, Cindy ^{[1
]}

Morozov, Pavel ^{[1
]}

Sajek, Marcin ^{[1
]}

Tuschl, Thomas ^{[1
]}

机构：

[1] Rockefeller Univ, Howard Hughes Med Inst, Lab RNA Mol Biol, 1230 York Ave, New York, NY 10065 USA

来源：

METHODS | 2017年 / 118卷

基金：

美国国家卫生研究院;

关键词：

Next-generation sequencing; UV RNA-protein crosslinking; Ribonucleoprotein analysis; Photocrosslinking; HETEROGENEOUS NUCLEAR-RNA; MESSENGER-RNA; COMPUTATIONAL APPROACH; CROSS-LINKING; TARGETS; SEQ; EXPRESSION; DATABASE; REVEALS; CELLS;

D O I：

10.1016/j.ymeth.2016.10.007

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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. (C) 2016 Elsevier Inc. All rights reserved.

引用

收藏

页码：24 / 40

页数：17

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