This volume presents a collection of versatile methodologies to investigate prokaryotic gene regulation, with focus on the different levels of information processing and usefulness for various model organisms, whether archaeal, bacterial, or both. The chapters in this book are divided into four sections. Section One covers methods that enable the study of the structure of the bacterial/archaeal chromosome, the main template for all gene regulatory processes, and its epigenetic modification. Section Two looks at a selection of approaches that enable higher levels of understanding of transcription initiation, a key step in information processing. Section Three discusses the investigation of regulating transcription factors, which are often considered the main players in gene regulation in prokaryotic cells. The Fourth Section focuses on the next stage of information processing at which gene regulation occurs, namely the RNA-based level. 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.

Cutting-edge and comprehensive, Prokaryotic Gene Regulation: Methods and Protocols is a valuable resource for researchers interested in learning more about this diverse field.

Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the experts

Inhalt
Chromosome Conformation Capture in Bacteria and Archaea.- Micrococcal Nuclease Digestion Assays for the Analysis of Chromosome Structure in Archaea.- Detecting DNA Methylations in the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius using SMRT-Sequencing.- ProD: A Tool for Predictive Design of Tailored Promoters in Escherichia coli.- Computational Study on the Dynamics of Mycobacterium Tuberculosis RNA Polymerase Assembly.- In Vitro Transcription Assay for Archaea Belonging to Sulfolobales.- Prediction of DNA-Binding Transcription Factors in Bacteria and Archaea Genomes.- In Vivo Screening Method for the Identification and Characterization of Prokaryotic, Metabolite-Responsive Transcription Factors.- Application of Special Electron Microscopy Techniques to the Study of DNA-Protein Complexes in E. coli Cells.- High-Speed Atomic Force Microscopy Visualization of Protein-DNA Interactions using DNA Origami Frames.- Separation and Characterization of Protein-DNA Complexes by EMSA and In-Gel Footprinting.- Chemical Protection and Premodification Binding Interference for the Identification of Phosphate and Base-Specific Contacts in Protein-DNA Complexes.- Analysis of Protein-DNA Interactions using Isothermal Titration Calorimetry: Successes and Failures.- Determination of RNA Structure with In Vitro SHAPE-Experiments.- Microscale Thermophoresis to Study RNA-RNA Binding Affinity.- Toeprint Assays for Detecting RNA Structure and Protein-RNA Interactions.