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Bacterial Regulatory RNA

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Véronique Arluison

    1. Université Paris Diderot & LLB/CEA/CNRS, Gif-sur-Yvette, France

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  2. Claudio Valverde

    1. Laboratorio de Bioquímica, Microbiología e Interacciones, Biológicas en el Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes-CONICET, Bernal, Argentina

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  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1737)

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Table of contents (21 protocols)

  1. Front Matter

    Pages i-xii
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  2. Identification of sRNA

    1. Front Matter

      Pages 1-1
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    2. Workflow for a Computational Analysis of an sRNA Candidate in Bacteria

      • Patrick R. Wright, Jens Georg
      Pages 3-30

    3. Guidelines for Inferring and Characterizing a Family of Bacterial trans-Acting Small Noncoding RNAs

      • Antonio Lagares Jr., Claudio Valverde
      Pages 31-45

    4. Bioinformatic Approach for Prediction of CsrA/RsmA-Regulating Small RNAs in Bacteria

      • Carl T. Fakhry, Kourosh Zarringhalam, Rahul V. Kulkarni
      Pages 47-56

  3. Function and Differential Expression of sRNA

    1. Front Matter

      Pages 57-57
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    2. Host-Pathogen Transcriptomics by Dual RNA-Seq

      • Alexander J. Westermann, Jörg Vogel
      Pages 59-75

    3. Identification of New Bacterial Small RNA Targets Using MS2 Affinity Purification Coupled to RNA Sequencing

      • Marie-Claude Carrier, Guillaume Laliberté, Eric Massé
      Pages 77-88

    4. Assessment of External Guide Sequences’ (EGS) Efficiency as Inducers of RNase P-Mediated Cleavage of mRNA Target Molecules

      • Saumya Jani, Alexis Jackson, Carol Davies-Sala, Kevin Chiem, Alfonso Soler-Bistué, Angeles Zorreguieta et al.
      Pages 89-98

    5. Evaluating the Effect of Small RNAs and Associated Chaperones on Rho-Dependent Termination of Transcription In Vitro

      • Cédric Nadiras, Annie Schwartz, Mildred Delaleau, Marc Boudvillain
      Pages 99-118

    6. Mapping Changes in Cell Surface Protein Expression Through Selective Labeling of Live Cells

      • Pierre Fechter
      Pages 119-127

    7. Fluorescence-Based Methods for Characterizing RNA Interactions In Vivo

      • Abigail N. Leistra, Mia K. Mihailovic, Lydia M. Contreras
      Pages 129-164

    8. Mutational Analysis of sRNA–mRNA Base Pairing by Electrophoretic Mobility Shift Assay

      • Eva Maria Sternkopf Lillebæk, Birgitte Haahr Kallipolitis
      Pages 165-176

    9. An Integrated Cell-Free Assay to Study Translation Regulation by Small Bacterial Noncoding RNAs

      • Erich Michel, Olivier Duss, Frédéric H.-T. Allain
      Pages 177-195

  4. Quantitation and Subcellular Localisation of sRNA

    1. Front Matter

      Pages 197-197
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    2. Quantitative Super-Resolution Imaging of Small RNAs in Bacterial Cells

      • Seongjin Park, Magda Bujnowska, Eric L. McLean, Jingyi Fei
      Pages 199-212

    3. Extraction and Analysis of RNA Isolated from Pure Bacteria-Derived Outer Membrane Vesicles

      • Janine Habier, Patrick May, Anna Heintz-Buschart, Anubrata Ghosal, Anke K. Wienecke-Baldacchino, Esther N. M. Nolte-‘t Hoen et al.
      Pages 213-230

    4. Absolute Regulatory Small Noncoding RNA Concentration and Decay Rates Measurements in Escherichia coli

      • Florent Busi, Véronique Arluison, Philippe Régnier
      Pages 231-248

  5. Cofactors of sRNA-Based Regulation

    1. Front Matter

      Pages 249-249
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    2. High-Resolution, High-Throughput Analysis of Hfq-Binding Sites Using UV Crosslinking and Analysis of cDNA (CRAC)

      • Brandon Sy, Julia Wong, Sander Granneman, David Tollervey, David Gally, Jai J. Tree
      Pages 251-272
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Keywords

About this book

This volume details the most important methods used for studying prokaryotic non-coding RNAs and their protein accomplices. Chapters present methods in sections covering different aspects of the biology of that field: identification of ncRNAs, their differential expression, characterization of their structure, abundance, intracellular location and function, their interaction with RNA binding proteins, and plausible applications of ncRNA elements in the rapidly emerging field of synthetic biology. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Bacterial Regulatory RNA: Methods and Protocols serves as a guidebook for scientists working toward the development of new tools and proceduresfor the vital field of sRNA biology.

Editors and Affiliations

  • Université Paris Diderot & LLB/CEA/CNRS, Gif-sur-Yvette, France

    Véronique Arluison

  • Laboratorio de Bioquímica, Microbiología e Interacciones, Biológicas en el Suelo, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes-CONICET, Bernal, Argentina

    Claudio Valverde

Bibliographic Information

  • Book Title: Bacterial Regulatory RNA

  • Book Subtitle: Methods and Protocols

  • Editors: Véronique Arluison, Claudio Valverde

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7634-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2018

  • Hardcover ISBN: 978-1-4939-7633-1Published: 27 February 2018

  • Softcover ISBN: 978-1-4939-9251-5Published: 10 December 2019

  • eBook ISBN: 978-1-4939-7634-8Published: 26 February 2018

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 395

  • Number of Illustrations: 22 b/w illustrations, 62 illustrations in colour

  • Topics: Human Genetics

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