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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.
List of contents
Determination of the 3D Genome Organization of Bacteria using Hi-C.- Overview of Processing and Analyzing Hi-C Data on Bacteria.- GeF-seq A Simple Procedure for Base Pair Resolution ChIP-seq.- Genomic SELEX Screening of Regulatory Targets of Escherichia coli Transcription Factors.- Modular assembly of Synthetic Secondary Chromosomes.- High-resolution Characterization of DNA/Protein Complexes in Living Bacteria.- Imaging of Transcription and Replication in the Bacterial Chromosome with Multicolor Three-dimensional Superresolution Structured Illumination Microscopy.- Genetic Approaches to Study the Interplay Between Transcription and Nucleoid-associated Proteins in Escherichia coliAtomic Force Microscopy Imaging and Analysis of Prokaryotic Genome Organization.- Dynamic Light Scattering of DNA-ligand Complexes.- Microscale Thermophoresis Analysis of Chromatin Interactions.- Quantitative Determination of DNA Bridging Efficiency of Chromatin Proteins.- Approaches for Determining DNA Persistence Length using Atomic Force Microscopy.- Quantitation of DNA Binding Affinity using Tethered Particle Motion.- Observing Bacterial Chromatin Protein-DNA Interactions by Combining DNA Flow-stretching with Single-molecule Imaging.- Unravelling the Biophysical Properties of Chromatin Proteins and DNA using Acoustic Force Spectroscopy.- Unravelling DNA organization with single-molecule Force Spectroscopy using Magnetic Tweezers.- In Vitro Transcription Assay to Quantify Effects of H-NS Filaments on RNA Chain Elongation by RNA Polymerase.- Deciphering 3D Organization Of Chromosomes using Hi-C Data.- Molecular Dynamics Simulation of a Feather-boa Model of Bacterial Chromosome.
