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This second edition brings together new and updated 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 key tips on troubleshooting and avoiding known pitfalls.
Authoritative and cutting-edge, Bacterial Chromatin: Methods and Protocols, Second Edition aims to be a useful up-to-date reference work for researchers currently in the field and to those entering the field.
Inhaltsverzeichnis
Shedding light on bacterial chromosome structure: exploring the significance of 3C-based approaches.- Circuit topology analysis of single cell Hi-C data.- GeF-seq: a simple procedure for base pair resolution ChIP-seq.- ChIP-qPCR of FLAG-tagged proteins in bacteria.- Genomic SELEX screening of regulatory targets of transcription factors.- High-resolution characterization of DNA/protein complexes in living bacteria.- High throughput mapping of bacterial chromosomal conformations using massively multiplexed Mu transposition.- In vivo genomic supercoiling mapping using Psora-seq.- Modular assembly of synthetic secondary chromosomes.- Visualization, quantification, and statistical evaluation of dynamics for DNA-binding proteins in bacteria by Single molecule tracking.- Genetic approaches to study the interplay between transcription and nucleoid-associated proteins in Escherichia coli.- Genetic engineering of Bacillus subtilis using competence-induced homologous recombination techniques.- Atomic force microscopy imaging and analysis of prokaryotic genome organization.- Atomic force microscopy characterisation of reconstituted protein-DNA complexes.- Approaches for determining DNA persistence length using Atomic Force Microscopy.- Dynamic light scattering of DNA-ligand complexes.- Microscale thermophoresis analysis of chromatin interactions.- In vitro transcription assay to quantify effects of H-NS filaments on RNA chain elongation by RNA polymerase.- Methods to quantitatively measure topological changes induced by DNA binding proteins in vivo and in vitro.- Quantitative determination of DNA bridging efficiency of chromatin proteins.- Measuring Partition Coefficients of in vitro Biomolecular Condensates using Fluorescence Correlation Spectroscopy.- Tethered Particle Motion analysis of the DNA binding properties of architectural proteins.- Quantitation of DNA binding affinity using Tethered Particle Motion.- Unravelling DNA organization with single-molecule Force Spectroscopy using Magnetic Tweezers.- Approaches to the full and partial chemical synthesis of proteins.- Deciphering Sequence-Specific DNA Binding by H-NS using Molecular Simulation.- Molecular dynamics simulations of a feather-boa model of a bacterial chromosome.- Replicating Chromosomes in Whole-Cell Models of Bacteria.
