Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions

Xiaoli Chen, Sarah A. Castro, Qiuying Liu, Wengian Hu, Shaojie Zhang

Research output: Contribution to journalArticle

Abstract

RNA-binding proteins are important players in post-transcriptional regulation, such as modulating mRNA splicing, translation, and degradation under diverse biological settings. Identifying and characterizing the RNA substrates is a critical step in deciphering the function and molecular mechanisms of the target RNA-binding proteins. High-throughput sequencing of the RNA fragments isolated by crosslinking immunoprecipitation (CLIP-seq) is one of the standard techniques to identify the in vivo transcriptome-wide binding sites of the target RNA-binding protein. This method is widely used in functional and mechanistic characterizations of RNA-binding proteins. In this review, we provide several practical considerations on performing and analyzing CLIP-seq experiments. Particularly, we focus on how to perform CLIP-seq experiments on endogenous RNA-binding proteins. In addition, we provide a practical summary on how to choose and use computational pipelines from an increasing number of computational methods and packages that are available for analyzing the sequencing datasets from the CLIP-seq experiments. We hope these practical considerations will facilitate experimental biologists in performing and analyzing CLIP-seq experiment to obtain biologically relevant mechanistic insights.

Original languageEnglish (US)
JournalMethods
DOIs
StateAccepted/In press - Jan 1 2018

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RNA-Binding Proteins
RNA
Proteins
Experiments
High-Throughput Nucleotide Sequencing
RNA Stability
Protein Biosynthesis
Computational methods
Transcriptome
Immunoprecipitation
Crosslinking
Pipelines
Binding Sites
Throughput
Degradation
Messenger RNA
Substrates

ASJC Scopus subject areas

  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions. / Chen, Xiaoli; Castro, Sarah A.; Liu, Qiuying; Hu, Wengian; Zhang, Shaojie.

In: Methods, 01.01.2018.

Research output: Contribution to journalArticle

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