Prokaryotic Gene Regulation: Methods and Protocols

ISBN-13: 9781071624128 / Angielski / Twarda / 2022

Peeters, Eveline

Opis

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.

Spis treści

Preface…
Table of Contents…
Contributing Authors…

1. Chromosome Conformation Capture in Bacteria and Archaea
Fatema-Zahra M. Rashid, Laurien Detmar, and Remus T. Dame

2. Micrococcal Nuclease Digestion Assays for the Analysis of Chromosome Structure in Archaea
Hugo Maruyama

3. Detecting DNA Methylations in the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius using SMRT-Sequencing
Christian Tellgren-Roth and Mohea Couturier

4. ProD: A Tool for Predictive Design of Tailored Promoters in Escherichia coli
Friederike Mey, Jim Clauwaert, Maarten Van Brempt, Michiel Stock, Jo Maertens, Willem Waegeman, and Marjan De Mey

5. Computational Study on the Dynamics of Mycobacterium Tuberculosis RNA Polymerase Assembly
Sneha Bheemireddy and Narayanaswamy Srinivasan

6. In Vitro Transcription Assay for Archaea Belonging to Sulfolobales
David Sybers, Daniel Charlier, and Eveline Peeters

7. Prediction of DNA-Binding Transcription Factors in Bacteria and Archaea Genomes
Leonardo Ledesma, Rafael Hernandez-Guerrero, and Ernesto Perez-Rueda

8. In Vivo Screening Method for the Identification and Characterization of Prokaryotic, Metabolite-Responsive Transcription Factors 
Amber Joka Bernauw, Veerke De Kock, and Indra Bervoets

9. Application of Special Electron Microscopy Techniques to the Study of DNA-Protein Complexes in E. coli Cells
Andrey Moiseenko, Natalia Loiko, Olga S. Sokolova, and Yurii F. Krupyanskii

10. High-Speed Atomic Force Microscopy Visualization of Protein-DNA Interactions using DNA Origami Frames
Ronnie G. Willaert and Sandor Kasas

11. Separation and Characterization of Protein-DNA Complexes by EMSA and In-Gel Footprinting
Daniel Charlier and Indra Bervoets

12. Chemical Protection and Premodification Binding Interference for the Identification of Phosphate and Base-Specific Contacts in Protein-DNA Complexes
Daniel Charlier

13. Analysis of Protein-DNA Interactions using Isothermal Titration Calorimetry: Successes and Failures
San Hadži and Jurij Lah

14. Determination of RNA Structure with In Vitro SHAPE-Experiments
Rani Baes, Daniel Charlier, and Eveline Peeters

15. Microscale Thermophoresis to Study RNA-RNA Binding Affinity
Britta Jordan, Lisa Nickel, and Ruth A. Schmitz

16. Toeprint Assays for Detecting RNA Structure and Protein-RNA Interactions
Helen Yakhnin and Paul Babitzke

Subject Index List…