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
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 DN
