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Bacterial Chromatin

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Remus T. Dame

    1. Leiden Institute of Chemistry and Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands

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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 1837)

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About this book

This volume brings together a wide range of methods to explore the structure and function of bacterial chromatin from molecular to the cellular scale. Chapters detail experimental protocols of in vivo and in vitro approaches, approaches to genome structure modeling, and data analysis. 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 Chromatin: Methods and Protocols aims to be useful as an up-to-date reference work for scholars in the bacterial chromatin field, those entering the field from adjacent research fields, and scientists in the eukaryotic chromatin field.

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Table of contents (20 protocols)

  1. Front Matter

    Pages i-xi
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  2. In Vivo Approaches

    1. Front Matter

      Pages 1-1
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    2. Determination of the 3D Genome Organization of Bacteria Using Hi-C

      • Frédéric G. Crémazy, Fatema-Zahra M. Rashid, James R. Haycocks, Lisa E. Lamberte, David C. Grainger, Remus T. Dame
      Pages 3-18

    3. Processing and Analysis of Hi-C Data on Bacteria

      • Andreas Hofmann, Dieter W. Heermann
      Pages 19-31

    4. GeF-seq: A Simple Procedure for Base Pair Resolution ChIP-seq

      • Onuma Chumsakul, Kensuke Nakamura, Shu Ishikawa, Taku Oshima
      Pages 33-47

    5. Genomic SELEX Screening of Regulatory Targets of Escherichia coli Transcription Factors

      • Tomohiro Shimada, Hiroshi Ogasawara, Akira Ishihama
      Pages 49-69

    6. Modular Assembly of Synthetic Secondary Chromosomes

      • Celine Zumkeller, Daniel Schindler, Torsten Waldminghaus
      Pages 71-94

    7. High-Resolution Characterization of DNA/Protein Complexes in Living Bacteria

      • Nicole A. Becker, Justin P. Peters, L. James Maher III
      Pages 95-115

    8. Imaging of Transcription and Replication in the Bacterial Chromosome with Multicolor Three-Dimensional Superresolution Structured Illumination Microscopy

      • Carmen Mata Martin, Cedric Cagliero, Zhe Sun, De Chen, Ding Jun Jin
      Pages 117-129

    9. Genetic Approaches to Study the Interplay Between Transcription and Nucleoid-Associated Proteins in Escherichia coli

      • Karin Schnetz
      Pages 131-143

  3. In Vitro Approaches

    1. Front Matter

      Pages 145-145
      Download chapter PDF

    2. Atomic Force Microscopy Imaging and Analysis of Prokaryotic Genome Organization

      • Ryosuke L. Ohniwa, Hugo Maruyama, Kazuya Morikawa, Kunio Takeyasu
      Pages 147-160

    3. Dynamic Light Scattering of DNA-Ligand Complexes

      • Guangcan Yang, Yanwei Wang
      Pages 161-176

    4. Microscale Thermophoresis Analysis of Chromatin Interactions

      • Ivan Corbeski, Velten Horn, Ramon A. van der Valk, Ulric B. le Paige, Remus T. Dame, Hugo van Ingen
      Pages 177-197

    5. Quantitative Determination of DNA Bridging Efficiency of Chromatin Proteins

      • Ramon A. van der Valk, Liang Qin, Geri F. Moolenaar, Remus T. Dame
      Pages 199-209

    6. Approaches for Determining DNA Persistence Length Using Atomic Force Microscopy

      • Justin P. Peters, L. James Maher III
      Pages 211-256

    7. Quantitation of DNA-Binding Affinity Using Tethered Particle Motion

      • Bram Henneman, Joost Heinsman, Julius Battjes, Remus T. Dame
      Pages 257-275

    8. Observing Bacterial Chromatin Protein-DNA Interactions by Combining DNA Flow-Stretching with Single-Molecule Imaging

      • HyeongJun Kim, Joseph J. Loparo
      Pages 277-299

    9. Unraveling the Biophysical Properties of Chromatin Proteins and DNA Using Acoustic Force Spectroscopy

      • Szu-Ning Lin, Liang Qin, Gijs J. L. Wuite, Remus T. Dame
      Pages 301-316

    10. Unraveling DNA Organization with Single-Molecule Force Spectroscopy Using Magnetic Tweezers

      • Thomas B. Brouwer, Artur Kaczmarczyk, Chi Pham, John van Noort
      Pages 317-349
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Editors and Affiliations

  • Leiden Institute of Chemistry and Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands

    Remus T. Dame

Bibliographic Information

  • Book Title: Bacterial Chromatin

  • Book Subtitle: Methods and Protocols

  • Editors: Remus T. Dame

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-8675-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

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

  • Hardcover ISBN: 978-1-4939-8674-3Published: 15 August 2018

  • Softcover ISBN: 978-1-4939-9362-8Published: 10 December 2019

  • eBook ISBN: 978-1-4939-8675-0Published: 14 August 2018

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 419

  • Number of Illustrations: 37 b/w illustrations, 81 illustrations in colour

  • Topics: Microbiology

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