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Transcriptome Data Analysis pp 171–182Cite as

Computational Analysis of RNA–Protein Interactions via Deep Sequencing

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1751))

Abstract

RNA-binding proteins (RBPs) function in all aspects of RNA processes including stability, structure, export, localization and translation, and control gene expression at the posttranscriptional level. To investigate the roles of RBPs and their direct RNA ligands in vivo, recent global approaches combining RNA immunoprecipitation and deep sequencing (RIP-seq) as well as UV-cross-linking (CLIP-seq) have become instrumental in dissecting RNA–protein interactions. However, the computational analysis of these high-throughput sequencing data is still challenging. Here, we provide a computational pipeline to analyze CLIP-seq and RIP-seq datasets. This generic analytic procedure may help accelerate the identification of direct RNA–protein interactions from high-throughput RBP profiling experiments in a variety of bacterial species.

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Acknowledgment

We thank Erik Holmqvist and Andrew Camilli for critical reading and comments on the manuscript.

Author information

Authors and Affiliations

  1. Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany

    Lei Li, Konrad U. Förstner & Yanjie Chao

  2. Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA

    Lei Li

  3. Department of Molecular Biology and Microbiology, Howard Hughes Medical Institute, Tufts University School of Medicine, Boston, MA, USA

    Yanjie Chao

Authors
  1. Lei Li
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  2. Konrad U. Förstner
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  3. Yanjie Chao
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Corresponding author

Correspondence to Yanjie Chao .

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Editors and Affiliations

  1. Department of Cell Biology and Genetics, School of Basic Medicine, Shenzhen University Health, Science Center, Shenzhen, China

    Yejun Wang

  2. Epigenomics and Computational Biology Lab, Biocomplexity Institute of Virginia Tech, Blacksburg, Virginia, USA

    Ming-an Sun

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Li, L., Förstner, K.U., Chao, Y. (2018). Computational Analysis of RNA–Protein Interactions via Deep Sequencing. In: Wang, Y., Sun, Ma. (eds) Transcriptome Data Analysis. Methods in Molecular Biology, vol 1751. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7710-9_12

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  • DOI: https://doi.org/10.1007/978-1-4939-7710-9_12

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7709-3

  • Online ISBN: 978-1-4939-7710-9

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