Bacterial Chromatin: Methods and Protocols

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 Transcription 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 Transcription 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 Transcription 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

11.              Microscale Thermophoresis Analysis of Chromatin Interactions

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

18.              In Vitro Transcription 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