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 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. 1. Determination of the 3D Genome Organization of Bacteria using Hi-C Frdric G. Crmazy, Fatema-Zahra M. Rashid, James R. Haycocks, Lisa E. Lamberte, David C. Grainger, and Remus T. Dame 2. Overview of Processing and Analyzing Hi-C Data on Bacteria Andreas Hofmann and Dieter W. Heermann 3. GeF-seq:A Simple Procedure for Base Pair Resolution ChIP-seq Onuma Chumsakul, Kensuke Nakamura, Shu Ishikawa, and Taku Oshima 4. Genomic SELEX Screening of Regulatory Targets of Escherichia coli Transcription Factors Tomohiro Shimada, Hiroshi Ogasawara, and Akira Ishihama 5. Modular assembly of Synthetic Secondary Chromosomes Celine Zumkeller, Daniel Schindler, and Torsten Waldminghaus 6. High-resolution Characterization of DNA/Protein Complexes in Living Bacteria Nicole A. Becker, Justin P. Peters, and L. James Maher, III 7. Imaging of Transcription and Replication in the Bacterial Chromosome with Multicolor Three-dimensional Superresolution Structured Illumination Microscopy Carmen Mata Martin, Cedric Cagliero, Zhe Sun, and Ding Jun Jin 8. Genetic Approaches to Study the Interplay Between Transcription and Nucleoid-associated Proteins in Escherichia coli Karin Schnetz Part I: In vitro approaches 9. Atomic Force Microscopy Imaging and Analysis of Prokaryotic Genome Organization Ryosuke L. Ohniwa, Hugo Maruyama, Kazuya Morikawa, and Kunio Takeyasu 10. Dynamic Light Scattering of DNA-ligand Complexes Guangcan Yang and Yanwei Wang 11. Microscale Thermophoresis Analysis of Chromatin Interactions Ivan Corbeski, Velten Horn, Ramon A. van der Valk, Ulric le Paige, Remus T. Dame, and Hugo van Ingen 12. Quantitative Determination of DNA Bridging Efficiency of Chromatin Proteins Ramon A. van der Valk, Qin Liang, Geri F. Moolenaar, and Remus T. Dame 13. Approaches for Determining DNA Persistence Length using Atomic Force Microscopy Justin P. Peters and L. James Maher, III 14. Quantitation of DNA Binding Affinity using Tethered Particle Motion Bram Henneman, Joost Heinsman, Julius Battjes, and Remus T. Dame 15. Observing Bacterial Chromatin Protein-DNA Interactions by Combining DNA Flow-stretching with Single-molecule Imaging HyeongJun Kim and Joseph J. Loparo 16. Unravelling the Biophysical Properties of Chromatin Proteins and DNA using Acoustic Force Spectroscopy Szu-Ning Lin, Liang Qin, Gijs J. L. Wuite and Remus T. Dame 17. Unravelling DNA organization with single-molecule Force Spectroscopy using Magnetic Tweezers Thomas B. Brouwer, Artur Kaczmarczyk, Chi Pham, and John van Noort 18. In Vitro Transcription Assay to Quantify Effects of H-NS Filaments on RNA Chain Elongation by RNA Polymerase Beth A. Boudreau, Matthew V. Kotlajich, and Robert Landick Part II: In Silico Approaches 19. Deciphering 3D Organization Of Chromosomes using Hi-C Data Andreas Hofmann and Dieter W. Heermann 20. Molecular Dynamics Simulation of a Feather-boa Model of Bacterial Chromosome Debasish Chaudhuri and Bela M. Mulder
