Transcriptome-wide identification of RNA binding sites by CLIP-seq

MurigneuxV.; SaulièreJ.; RoestCrolliusH.; LeHirH.

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Transcriptome-wide identification of RNA binding sites by CLIP-seq

机译：通过CLIP-seq在转录组范围内鉴定RNA结合位点

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An emergent strategy for the transcriptome-wide study of protein-RNA interactions is CLIP-seq (crosslinking and immunoprecipitation followed by high-throughput sequencing). We combined CLIP-seq and mRNA-seq to identify direct RNA binding sites of eIF4AIII in human cells. This RNA helicase is a core constituant of the Exon Junction Complex (EJC), a multifunctional protein complex associated with spliced mRNAs in metazoans. Here, we describe the successive steps of the CLIP protocol and the computational tools and strategies we employed to map the physiological targets of eIF4AIII on human RNAs.

机译：全转录组研究蛋白质-RNA相互作用的一种新兴策略是CLIP-seq（交联和免疫沉淀，然后进行高通量测序）。我们结合了CLIP-seq和mRNA-seq，以鉴定人类细胞中eIF4AIII的直接RNA结合位点。这种RNA解旋酶是外显子连接复合物（EJC）的核心成分，该复合物是与后生动物中剪接的mRNA相关的多功能蛋白质复合物。在这里，我们描述了CLIP协议的后续步骤以及我们用来在人类RNA上绘制eIF4AIII生理学靶标的计算工具和策略。

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《Methods: A Companion to Methods in Enzymology》 |2013年第1期|共9页
作者
MurigneuxV.; SaulièreJ.; RoestCrolliusH.; LeHirH.;
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原文格式 PDF
正文语种 eng
中图分类生物化学;
关键词
Bioinformatics; CLIP; Next-generation sequencing; Protein-RNA interactions;

机译：生物信息学;CLIP;下一代测序;蛋白质-RNA相互作用;

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1. Transcriptome-wide identification of RNA binding sites by CLIP-seq [J] . MurigneuxV., SaulièreJ., RoestCrolliusH., Methods: A Companion to Methods in Enzymology . 2013,第1期

机译：通过CLIP-seq在转录组范围内鉴定RNA结合位点
2. In vivo and transcriptome-wide identification of RNA binding protein target sites. [J] . Jungkamp AC, Stoeckius M, Mecenas D, Molecular cell . 2011,第5期

机译：在体内和转录组范围内鉴定RNA结合蛋白靶位点。
3. Statistical issues in binding site identification through CLIP-seq [J] . Chen Xiaowei, Chung Dongjun, Stefani Giovanni, Statistics and Its Interface . 2015,第4期

机译：通过CLIP-seq识别结合位点的统计问题
4. Identification of functional genetic variants in miRNA binding site in genes associated with lung cancer [C] . Anju Gupta, Priyanka Kumari, Mottadi Shiva, 2016 International Conference on Bioinformatics and Systems Biology . 2016

机译：肺癌相关基因miRNA结合位点功能性遗传变异的鉴定
5. Identification and structural characterization of a high-affinity nucleocapsid protein binding site within the Moloney murine leukemia virus Psi-RNA packaging signal: Implications for genome recognition. [D] . D'Souza, Victoria Manuel. 2002

机译：莫洛尼鼠白血病病毒Psi-RNA包装信号中高亲和力核衣壳蛋白结合位点的鉴定和结构表征：对基因组识别的影响。
6. Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins [O] . Aitor Garzia, Cindy Meyer, Pavel Morozov, -1

机译：PAR-CLIP的优化用于在转录组范围内鉴定RNA结合蛋白的结合位点
7. Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins [O] . Aitor Garzia, Cindy Meyer, Pavel Morozov, 2017

机译：RNA结合蛋白结合位点的转录综合剪辑优化

Transcriptome-wide identification of RNA binding sites by CLIP-seq

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