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Dissecting Splicing Regulatory Network by Integrative Analysis of CLIP-Seq Data

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Abstract

Detecting protein–RNA interaction and identifying RNA-binding protein (RBP) targets on a global scale have become increasingly important for understanding RNA regulatory mechanisms and reverse-engineering RNA regulation network at systems level. Significant progress was made in the past few years. Cross-linking and immunoprecipitation (CLIP) coupled with high-throughput sequencing (HITS) the method of choice for transcriptome-wide coverage as well as for high-resolution mapping of RBP sites and for in vivo target identification. In this chapter, we introduce the current status of the technology, with a focus on bioinformatic analysis of HITS-CLIP or CLIP-seq data, in understanding RNA splicing regulation network through building RNA splicing maps.

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Author information

Authors and Affiliations

  1. Department of Molecular and Cell Biology, Center for Systems Biology, The University of Texas at Dallas, RL11, 800 West Campbell Road, Richardson, TX, 75080, USA

    Michael Q. Zhang

  2. Bioinformatics Division, TNLIST, Tsinghua University, Beijing, 100084, China

    Michael Q. Zhang

Authors
  1. Michael Q. Zhang
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Correspondence to Michael Q. Zhang .

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Editors and Affiliations

  1. CIC bioGUNE, Genome Analysis Platform, Derio, 48160, Spain

    Naiara Rodríguez-Ezpeleta

  2. Computational Genomics and Bioinformatic, University of Granada, Genetics Department & Biomedical Research Center (CIBM), Granada, Spain

    Michael Hackenberg

  3. CIC bioGUNE, Genome Analysis Platform, Derio, 48160, Spain

    Ana M. Aransay

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Zhang, M.Q. (2012). Dissecting Splicing Regulatory Network by Integrative Analysis of CLIP-Seq Data. In: Rodríguez-Ezpeleta, N., Hackenberg, M., Aransay, A. (eds) Bioinformatics for High Throughput Sequencing. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-0782-9_12

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