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Bacterial Transcriptional Control

Methods and Protocols

  • Book
  • © 2015

Overview

Editors:
  1. Irina Artsimovitch

    1. Department of Microbiology, The Ohio State University, Columbus, USA

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    You can also search for this editor in PubMed   Google Scholar

  2. Thomas J. Santangelo

    1. Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • 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 1276)

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Table of contents (20 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Mapping the Escherichia coli Transcription Elongation Complex with Exonuclease III

    • Zhaokun Liu, Irina Artsimovitch
    Pages 1-12

  3. Purification of Bacterial RNA Polymerase: Tools and Protocols

    • Vladimir Svetlov, Irina Artsimovitch
    Pages 13-29

  4. Monitoring Translocation of Multisubunit RNA Polymerase Along the DNA with Fluorescent Base Analogues

    • Anssi M. Malinen, Matti Turtola, Georgiy A. Belogurov
    Pages 31-51

  5. In Vitro and In Vivo Methodologies for Studying the Sigma 54-Dependent Transcription

    • Martin Buck, Christoph Engl, Nicolas Joly, Goran Jovanovic, Milija Jovanovic, Edward Lawton et al.
    Pages 53-79

  6. Methods for the Assembly and Analysis of In Vitro Transcription-Coupled-to-Translation Systems

    • Daniel Castro-Roa, Nikolay Zenkin
    Pages 81-99

  7. Site-Specific Incorporation of Probes into RNA Polymerase by Unnatural-Amino-Acid Mutagenesis and Staudinger–Bertozzi Ligation

    • Anirban Chakraborty, Abhishek Mazumder, Miaoxin Lin, Adam Hasemeyer, Qumiao Xu, Dongye Wang et al.
    Pages 101-131

  8. Reconstitution of Factor-Dependent, Promoter Proximal Pausing in Drosophila Nuclear Extracts

    • Jian Li, David S. Gilmour
    Pages 133-152

  9. Direct Competition Assay for Transcription Fidelity

    • Lucyna Lubkowska, Maria L. Kireeva
    Pages 153-164

  10. Single-Stranded DNA Aptamers for Functional Probing of Bacterial RNA Polymerase

    • Danil Pupov, Andrey Kulbachinskiy
    Pages 165-183

  11. Biochemical Analysis of Transcription Termination by RNA Polymerase III from Yeast Saccharomyces cerevisiae

    • Aneeshkumar G. Arimbasseri, Richard J. Maraia
    Pages 185-198

  12. Use of RNA Polymerase Molecular Beacon Assay to Measure RNA Polymerase Interactions with Model Promoter Fragments

    • Vladimir Mekler, Konstantin Severinov
    Pages 199-210

  13. Preparation of cDNA Libraries for High-Throughput RNA Sequencing Analysis of RNA 5′ Ends

    • Irina O. Vvedenskaya, Seth R. Goldman, Bryce E. Nickels
    Pages 211-228

  14. In Situ Footprinting of E. coli Transcription Elongation Complex with Chloroacetaldehyde

    • A. Rachid Rahmouni, Christine Mosrin-Huaman
    Pages 229-240

  15. Using Solutes and Kinetics to Probe Large Conformational Changes in the Steps of Transcription Initiation

    • Emily F. Ruff, Wayne S. Kontur, M. Thomas Record Jr.
    Pages 241-261

  16. Manipulating Archaeal Systems to Permit Analyses of Transcription Elongation-Termination Decisions In Vitro

    • Alexandra M. Gehring, Thomas J. Santangelo
    Pages 263-279

  17. Purification of Active RNA Polymerase I from Yeast

    • Francis Dean Appling, David Alan Schneider
    Pages 281-289

  18. Transcription in Archaea: Preparation of Methanocaldococcus jannaschii Transcription Machinery

    • Katherine Smollett, Fabian Blombach, Finn Werner
    Pages 291-303

  19. Transcription in Archaea: In Vitro Transcription Assays for mjRNAP

    • Katherine Smollett, Fabian Blombach, Finn Werner
    Pages 305-314

  20. Experimental Analysis of hFACT Action During Pol II Transcription In Vitro

    • Fu-Kai Hsieh, Olga I. Kulaeva, Vasily M. Studitsky
    Pages 315-326
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Keywords

About this book

This volume is designed to be a resource of proven techniques and approaches for probing the activities of bacterial, eukaryotic, and archaeal RNA polymerases. This book features a collection of in vitro and in vivo technologies that will permit researchers to purify and probe the position and stability of RNA polymerase complexes at different points of the transcription cycle, analyze the various translocations and intermolecular movements associated with catalysis, define recruitment strategies, probe the roles of transcription factors in each stage of the cycle, highlight conserved and disparate fidelity mechanisms, analyze the resultant transcripts, and study coordination of the nascent mRNA synthesis by the RNA polymerase and mRNA translation by the ribosome. Written in the highly successful Methods of 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 key tips on troubles troubleshooting and avoiding known pitfalls.

Practical and timely, Bacterial Transcriptional Controls: Methods and Protocols highlights the breadth and depth of techniques that are likely to continue shaping the transcription community in the future.

Editors and Affiliations

  • Department of Microbiology, The Ohio State University, Columbus, USA

    Irina Artsimovitch

  • Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, USA

    Thomas J. Santangelo

About the editors

Name: Irina Artsimovitch Address: Department of Microbiology The Ohio State University 484 West 12th Avenue Columbus, OH 43210 Phone: (614) 292-6777 Email: artsimovitch.1@osu.edu

Bibliographic Information

  • Book Title: Bacterial Transcriptional Control

  • Book Subtitle: Methods and Protocols

  • Editors: Irina Artsimovitch, Thomas J. Santangelo

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-2392-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2015

  • Hardcover ISBN: 978-1-4939-2391-5Published: 10 February 2015

  • Softcover ISBN: 978-1-4939-5467-4Published: 05 October 2016

  • eBook ISBN: 978-1-4939-2392-2Published: 09 February 2015

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 342

  • Number of Illustrations: 23 b/w illustrations, 25 illustrations in colour

  • Topics: Microbiology, Bacteriology, Genetic Engineering

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