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Bacterial Regulatory RNA

Methods and Protocols

  • Book
  • © 2012

Overview

Editors:
  1. Kenneth C. Keiler

    1. , Dept. of Biochemistry and Molecular Biol, The Pennsylvania State University, University Park, USA

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  • Collects vital methods for identification of bacterial regulatory RNAs and characterization of their biochemical properties and activities
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 905)

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Table of contents (20 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Identification of Regulatory RNAs

    1. Front Matter

      Pages 1-1
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    2. Bioinformatic Discovery of Bacterial Regulatory RNAs Using SIPHT

      • Jonathan Livny
      Pages 3-14

    3. How to Identify CRISPRs in Sequencing Data

      • Christine Drevet, Christine Pourcel
      Pages 15-27

    4. A Strategy for Identifying Noncoding RNAs Using Whole-Genome Tiling Arrays

      • Stephen G. Landt, Eduardo Abeliuk
      Pages 29-39

    5. Genetic Screens to Identify Bacterial sRNA Regulators

      • Pierre Mandin
      Pages 41-60

  3. Function and Expression of Regulatory RNAs

    1. Front Matter

      Pages 61-61
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    2. Competition Assays Using Barcoded Deletion Strains to Gain Insight into Small RNA Function

      • Errett C. Hobbs, Gisela Storz
      Pages 63-72

    3. Use of Semi-quantitative Northern Blot Analysis to Determine Relative Quantities of Bacterial CRISPR Transcripts

      • Ksenia Pougach, Konstantin Severinov
      Pages 73-86

    4. RNA Visualization in Bacteria by Fluorescence In Situ Hybridization

      • Jay H. Russell, Kenneth C. Keiler
      Pages 87-95

  4. RNA Structure and Biophysical Measurements

    1. Front Matter

      Pages 97-97
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    2. RNA Structure Prediction: An Overview of Methods

      • Matthew G. Seetin, David H. Mathews
      Pages 99-122

    3. Crystallization of RNA–Protein Complexes: From Synthesis and Purification of Individual Components to Crystals

      • Anna Perederina, Andrey S. Krasilnikov
      Pages 123-143

    4. Analysis of RNA Folding and Ligand Binding by Conventional and High-Throughput Calorimetry

      • Joshua E. Sokoloski, Philip C. Bevilacqua
      Pages 145-174

  5. RNA–Protein Interactions

    1. Front Matter

      Pages 175-175
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  6. RNA-Protein Interactions

    1. Use of Aptamer Tagging to Identify In Vivo Protein Binding Partners of Small Regulatory RNAs

      • Colin P. Corcoran, Renate Rieder, Dimitri Podkaminski, Benjamin Hofmann, Jörg Vogel
      Pages 177-200

    2. Gel Mobility Shift Assays to Detect Protein–RNA Interactions

      • Alexander V. Yakhnin, Helen Yakhnin, Paul Babitzke
      Pages 201-211

    3. RNase Footprinting of Protein Binding Sites on an mRNA Target of Small RNAs

      • Yi Peng, Toby J. Soper, Sarah A. Woodson
      Pages 213-224

  7. RNA–RNA Interactions

    1. Front Matter

      Pages 225-225
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  8. RNA-RNA Interactions

    1. Computational Identification of sRNA Targets

      • Brian Tjaden
      Pages 227-234
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Keywords

About this book

The discovery of wide-spread RNA-based regulation in bacteria has led to new evaluations of the importance of bacterial regulatory RNA in every aspect of bacterial physiology. In Bacteria Regulatory RNA: Methods and Protocols, expert researchers in the field detail many of the methods which are now commonly used to study bacterial regulatory RNA. These include methods and techniques to identify regulatory RNAs, characterizing the function and expression of regulatory RNAs in bacterial cells, RNA structure prediction, and interactions between regulatory RNAs and proteins. Written in the highly successful Methods in Molecular Biologyâ„¢ series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.

 

 Authoritative and practical, Bacteria Regulatory RNA: Methods and Protocols seeks to aid scientists in the further study of bacterial regulatory RNA.

Editors and Affiliations

  • , Dept. of Biochemistry and Molecular Biol, The Pennsylvania State University, University Park, USA

    Kenneth C. Keiler

Bibliographic Information

  • Book Title: Bacterial Regulatory RNA

  • Book Subtitle: Methods and Protocols

  • Editors: Kenneth C. Keiler

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-61779-949-5

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2012

  • Hardcover ISBN: 978-1-61779-948-8Published: 28 June 2012

  • Softcover ISBN: 978-1-4939-5941-9Published: 23 August 2016

  • eBook ISBN: 978-1-61779-949-5Published: 27 June 2012

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 333

  • Topics: Human Genetics, Microbial Genetics and Genomics

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