Bacterial transcriptional control : methods and protocols

Bibliographic Information

Bacterial transcriptional control : methods and protocols

edited by Irina Artsimovitch, Thomas J. Santangelo

(Methods in molecular biology / John M. Walker, series editor, 1276)(Springer protocols)

Humana Press, c2015

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Includes bibliographical references and index

Description and Table of Contents

Description

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.

Table of Contents

1. Mapping the Escherichia coli Transcription Elongation Complex with Exonuclease III Zhaokun Liu and Irina Artsimovitch 2. Purification of Bacterial RNA Polymerase: Tools and Protocols Vladimir Svetlov and Irina Artsimovitch 3. Monitoring Translocation of Multisubunit RNA Polymerase Along the DNA with Fluorescent Base Analogues Anssi M. Malinen, Matti Turtola, and Georgiy A. Belogurov 4. In vitro and in vivo Methodologies for Studying the Sigma54-dependent Transcription Martin Buck, Christoph Engl, Nicolas Joly, Goran Jovanovic, Milija Jovanovic, Edward Lawton, Christopher McDonald, Joerg Schumacher, Christopher Waite, and Nan Zhang 5. Methods for the Assembly and Analysis of in vitro Transcription-coupled-to-translation Systems Daniel Castro-Roa and Nikolay Zenkin 6. 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, Yon W. Ebright, and Richard H. Ebright 7. Reconstitution of Factor-dependent, Promoter Proximal Pausing in Drosophila Nuclear Extracts Jian Li and David S. Gilmour 8. Direct Competition Assay for Transcription Fidelity Lucyna Lubkowska and Maria L. Kireeva 9. Single-stranded DNA Aptamers for Functional Probing of Bacterial RNA Polymerase Danil Pupov and Andrey Kulbachinskiy 10. Biochemical Analysis of Transcription Termination by RNA Polymerase III from Yeast Saccharomyces cerevisiae Aneeshkumar G. Arimbasseri and Richard J. Maraia 11. Use of RNA Polymerase Molecular Beacon Assay to Measure RNA Polymerase Interactions with Model Promoter Fragments Vladimir Mekler and Konstantin Severinov 12. Preparation of cDNA Libraries for High-throughput RNA Sequencing Analysis of RNA 5' Ends Irina O. Vvedenskaya, Seth R. Goldman, and Bryce E. Nickels 13. In situ Footprinting of E. coli Transcription Elongation Complex with Chloroacetaldehyde A. Rachid Rahmouni and Christine Mosrin-Huaman 14. Using Solutes and Kinetics to Probe Large Conformational Changes in the Steps of Transcription Initiation Emily Ruff, Wayne S. Kontur, and M. Thomas Record Jr. 15. Manipulating Archaeal Systems to Permit Analyses of Transcription Elongation-termination Decisions in vitro Alexandra M. Gehring and Thomas J. Santangelo 16. Purification of Active RNA Polymerase I from Yeast Francis Dean Appling and David Alan Schneider 17. Transcription in Archaea: preparation of Methanocaldococcus jannaschii Transcription Machinery Katherine Smollett, Fabian Blombach, and Finn Werner 18. Transcription in Archaea: in vitro Transcription Assays for mjRNAP Katherine Smollett, Fabian Blombach, and Finn Werner 19. Experimental Analysis of hFACT Action during Pol II Transcription in vitro Fu-Kai Hsieh, Olga I. Kulaeva, and Vasily M. Studitsky 20. ChIP-seq for Genome-scale Analysis of Bacterial DNA-binding Proteins Richard P. Bonocora and Joseph T. Wade

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