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Characterization of the B Cell Transcriptome Bound by RNA-Binding Proteins with iCLIP

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Book cover Germinal Centers

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1623))

Abstract

Posttranscriptional regulation of gene expression shapes the B cell transcriptome and controls messenger RNA (mRNA) translation into protein. Recent reports have highlighted the importance of RNA binding proteins (RBPs) for mRNA splicing, subcellular location, stability, and translation during B lymphocyte development, activation, and differentiation. Here we describe individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) in primary lymphocytes, a method that maps RNA–protein interactions in a genome-wide scale allowing mechanistic analysis of RBP function. We discuss the latest improvements in iCLIP technology and provide some examples of how integration of the RNA–protein interactome with other high-throughput mRNA sequencing methodologies uncovers the important role of RBP-mediated RNA regulation in key biological cell processes.

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Acknowledgments

We thank Prof. Jernej Ule and Prof. Tomaz Curk for their valuable contribution in experimental setup and analysis. The authors were supported by a Biotechnology and Biological Sciences Research Council strategic Lola grant BB/J00152X/1 and program funding BBS/E/B/000C0409.

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Authors and Affiliations

  1. Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, CB22 3AT, UK

    Manuel D. Díaz-Muñoz, Elisa Monzón-Casanova & Martin Turner

  2. Department of Immunobiology, Division of Immunology, Infection and Inflammatory Disease, King’s College London, SE1 9RT, London, UK

    Manuel D. Díaz-Muñoz

  3. Department of Biochemistry, University of Cambridge, Cambridge, UK

    Elisa Monzón-Casanova

Authors
  1. Manuel D. Díaz-Muñoz
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  2. Elisa Monzón-Casanova
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  3. Martin Turner
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Corresponding authors

Correspondence to Manuel D. Díaz-Muñoz or Martin Turner .

Editor information

Editors and Affiliations

  1. Immunity and Cancer Laboratory, The Francis Crick Institute, and King’s College London, London, United Kingdom

    Dinis Pedro Calado

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Díaz-Muñoz, M.D., Monzón-Casanova, E., Turner, M. (2017). Characterization of the B Cell Transcriptome Bound by RNA-Binding Proteins with iCLIP. In: Calado, D. (eds) Germinal Centers. Methods in Molecular Biology, vol 1623. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7095-7_14

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  • DOI: https://doi.org/10.1007/978-1-4939-7095-7_14

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  • Publisher Name: Humana Press, New York, NY

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