Bacterial Chromatin: Methods and Protocols

Description

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 beuseful 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. Front Matter ....Pages i-xi Front Matter ....Pages 1-1 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 Processing and Analysis of Hi-C Data on Bacteria (Andreas Hofmann, Dieter W. Heermann)....Pages 19-31 GeF-seq: A Simple Procedure for Base Pair Resolution ChIP-seq (Onuma Chumsakul, Kensuke Nakamura, Shu Ishikawa, Taku Oshima)....Pages 33-47 Genomic SELEX Screening of Regulatory Targets of Escherichia coli Transcription Factors (Tomohiro Shimada, Hiroshi Ogasawara, Akira Ishihama)....Pages 49-69 Modular Assembly of Synthetic Secondary Chromosomes (Celine Zumkeller, Daniel Schindler, Torsten Waldminghaus)....Pages 71-94 High-Resolution Characterization of DNA/Protein Complexes in Living Bacteria (Nicole A. Becker, Justin P. Peters, L. James Maher III)....Pages 95-115 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 Genetic Approaches to Study the Interplay Between Transcription and Nucleoid-Associated Proteins in Escherichia coli (Karin Schnetz)....Pages 131-143 Front Matter ....Pages 145-145 Atomic Force Microscopy Imaging and Analysis of Prokaryotic Genome Organization (Ryosuke L. Ohniwa, Hugo Maruyama, Kazuya Morikawa, Kunio Takeyasu)....Pages 147-160 Dynamic Light Scattering of DNA-Ligand Complexes (Guangcan Yang, Yanwei Wang)....Pages 161-176 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 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 Approaches for Determining DNA Persistence Length Using Atomic Force Microscopy (Justin P. Peters, L. James Maher III)....Pages 211-256 Quantitation of DNA-Binding Affinity Using Tethered Particle Motion (Bram Henneman, Joost Heinsman, Julius Battjes, Remus T. Dame)....Pages 257-275 Observing Bacterial Chromatin Protein-DNA Interactions by Combining DNA Flow-Stretching with Single-Molecule Imaging (HyeongJun Kim, Joseph J. Loparo)....Pages 277-299 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 Unraveling DNA Organization with Single-Molecule Force Spectroscopy Using Magnetic Tweezers (Thomas B. Brouwer, Artur Kaczmarczyk, Chi Pham, John van Noort)....Pages 317-349 In Vitro Transcription Assay to Quantify Effects of H-NS Filaments on RNA Chain Elongation by RNA Polymerase (Beth A. Boudreau, Matthew V. Kotlajich, Robert Landick)....Pages 351-386 Front Matter ....Pages 387-387 Deciphering 3D Organization of Chromosomes Using Hi-C Data (Andreas Hofmann, Dieter W. Heermann)....Pages 389-401 Molecular Dynamics Simulation of a Feather-Boa Model of a Bacterial Chromosome (Debasish Chaudhuri, Bela M. Mulder)....Pages 403-415 Back Matter ....Pages 417-419