Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
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.
1. Determination of the 3D Genome Organization of Bacteria using Hi-C
Frédéric G. Crémazy, Fatema-Zahra M. Rashid, James R. Haycocks, Lisa E. Lamberte, David C. Grainger, and Remus T. Dame
2. Overview of Processing and Analyzing Hi-C Data on Bacteria
Andreas Hofmann and Dieter W. Heermann
3. GeF-seq:A Simple Procedure for Base Pair Resolution ChIP-seq
Onuma Chumsakul, Kensuke Nakamura, Shu Ishikawa, and Taku Oshima
4. Genomic SELEX Screening of Regulatory Targets of Escherichia coli Tranillegalscription Factors
Tomohiro Shimada, Hiroshi Ogasawara, and Akira Ishihama
5. Modular assembly of Synthetic Secondary Chromosomes
Celine Zumkeller, Daniel Schindler, and Torsten Waldminghaus
6. High-resolution Characterization of DNA/Protein Complexes in Living Bacteria
Nicole A. Becker, Justin P. Peters, and L. James Maher, III
7. Imaging of Tranillegalscription and Replication in the Bacterial Chromosome with Multicolor Three-dimensional Superresolution Structured Illumination Microscopy
Carmen Mata Martin, Cedric Cagliero, Zhe Sun, and Ding Jun Jin
8. Genetic Approaches to Study the Interplay Between Tranillegalscription and Nucleoid-associated Proteins in Escherichia coli
Karin Schnetz
Part I: In vitro approaches
9. Atomic Force Microscopy Imaging and Analysis of Prokaryotic Genome Organization
Ryosuke L. Ohniwa, Hugo Maruyama, Kazuya Morikawa, and Kunio Takeyasu
10. Dynamic Light Scattering of DNA-ligand Complexes
Guangcan Yang and Yanwei Wang
11. Microscale Thermophoresis Analysis of Chromatin Interactions
Ivan Corbeski, Velten Horn, Ramon A. van der Valk, Ulric le Paige, Remus T. Dame,
and Hugo van Ingen
12. Quantitative Determination of DNA Bridging Efficiency of Chromatin Proteins
Ramon A. van der Valk, Qin Liang, Geri F. Moolenaar, and Remus T. Dame
13. Approaches for Determining DNA Persistence Length using Atomic Force Microscopy
Justin P. Peters and L. James Maher, III
14. Quantitation of DNA Binding Affinity using Tethered Particle Motion
Bram Henneman, Joost Heinsman, Julius Battjes, and Remus T. Dame
15. Observing Bacterial Chromatin Protein-DNA Interactions by Combining DNA Flow-stretching with Single-molecule Imaging
HyeongJun Kim and Joseph J. Loparo
16. Unravelling the Biophysical Properties of Chromatin Proteins and DNA using Acoustic Force Spectroscopy
Szu-Ning Lin, Liang Qin, Gijs J. L. Wuite and Remus T. Dame
17. Unravelling DNA organization with single-molecule Force Spectroscopy using Magnetic Tweezers
Thomas B. Brouwer, Artur Kaczmarczyk, Chi Pham, and John van Noort
18. In Vitro Tranillegalscription Assay to Quantify Effects of H-NS Filaments on RNA Chain Elongation by RNA Polymerase
Beth A. Boudreau, Matthew V. Kotlajich, and Robert Landick
Part II: In Silico Approaches
19. Deciphering 3D Organization Of Chromosomes using Hi-C Data
Andreas Hofmann and Dieter W. Heermann
20. Molecular Dynamics Simulation of a Feather-boa Model of Bacterial Chromosome
Debasish Chaudhuri and Bela M. Mulder
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.
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 Tranillegalscription Factors.- Modular assembly of Synthetic Secondary Chromosomes.- High-resolution Characterization of DNA/Protein Complexes in Living Bacteria.- Imaging of Tranillegalscription and Replication in the Bacterial Chromosome with Multicolor Three-dimensional Superresolution Structured Illumination Microscopy.- Genetic Approaches to Study the Interplay Between Tranillegalscription 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 Tranillegalscription 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.
Inhaltsverzeichnis
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 Tranillegalscription Factors.- Modular assembly of Synthetic Secondary Chromosomes.- High-resolution Characterization of DNA/Protein Complexes in Living Bacteria.- Imaging of Tranillegalscription and Replication in the Bacterial Chromosome with Multicolor Three-dimensional Superresolution Structured Illumination Microscopy.- Genetic Approaches to Study the Interplay Between Tranillegalscription 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 Tranillegalscription 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.
Klappentext
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.nAuthoritative 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.
Includes cutting-edge methods and protocols
Provides step-by-step detail essential for reproducible results
Contains key notes and implementation advice from the experts
