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CLIP-Seq in Bacteria: Global Recognition Patterns of Bacterial RNA-Binding Proteins
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology. Uppsala Univ, Biomed Ctr, Dept Cell & Mol Biol, Uppsala, Sweden.
2018 (English)In: High-Density Sequencing Applications in Microbial Molecular Genetics / [ed] Carpousis, A J, ELSEVIER ACADEMIC PRESS INC , 2018, p. 127-145Chapter in book (Refereed)
Abstract [en]

RNA-protein interactions are at the heart of many central cellular processes, and RNA-binding proteins (RBPs) associate with virtually all RNA molecules in a cell. In bacteria, global RBPs, often in conjunction with small regulatory RNAs, affect physiology and virulence by controlling transcription, translation, and RNA decay. To understand how these regulatory proteins orchestrate global gene expression, detailed maps of their cellular RNA binding sites are required. To this end, cross-linking and immunoprecipitation followed by deep sequencing (CLIP-seq) has revolutionized RBP studies by providing knowledge about global recognition patterns of RBPs in both eukaryotic and bacterial cells. In this chapter, we provide a step-by-step protocol for global mapping of bona fide RBP binding sites using CLIP-seq in bacteria. This protocol has been successfully applied for charting the binding sites of Hfq, CsrA, and ProQ, three global regulatory RBPs in Salmonella enterica and Escherichia coli, and should be readily applicable to other RBPs and bacterial species.

Place, publisher, year, edition, pages
ELSEVIER ACADEMIC PRESS INC , 2018. p. 127-145
Series
Methods in Enzymology, ISSN 0076-6879 ; 612
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-373556DOI: 10.1016/bs.mie.2018.08.008ISI: 000452368600007PubMedID: 30502939ISBN: 978-0-12-815993-4 (print)OAI: oai:DiVA.org:uu-373556DiVA, id: diva2:1279587
Available from: 2019-01-17 Created: 2019-01-17 Last updated: 2019-01-17Bibliographically approved

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Andresen, LiisHolmqvist, Erik

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