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.