Bacterial Chromatin: Methods and Protocols

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