Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Badel, C., Samson, R. Y. & Bell, S. D. Chromosome organization affects genome evolution in Sulfolobus archaea. Nat. Microbiol. 7, 820–830 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Marinov, G. K. et al. The chromatin landscape of the euryarchaeon Haloferax volcanii. Genome Biol. 24, 253 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Whitfield, C. R., Wardle, S. J. & Haniford, D. B. The global bacterial regulator H-NS promotes transpososome formation and transposition in the Tn5 system. Nucleic Acids Res. 37, 309–321 (2009).

Article  CAS  PubMed  Google Scholar 

Kelly, T. K. et al. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res. 22, 2497–2506 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tavazoie, S. & Church, G. M. Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli. Nat. Biotechnol. 16, 566–571 (1998).

Article  CAS  PubMed  Google Scholar 

Vora, T., Hottes, A. K. & Tavazoie, S. Protein occupancy landscape of a bacterial genome. Mol. Cell 35, 247–253 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Freddolino, L., Amemiya, H. M., Goss, T. J. & Tavazoie, S. Dynamic landscape of protein occupancy across the Escherichia coli chromosome. PLoS Biol. 19, e3001306 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Amemiya, H. M., Schroeder, J. & Freddolino, L. Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. Transcription 12, 182–218 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306–2309 (2000).

Article  CAS  PubMed  Google Scholar 

Park, P. J. ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet. 10, 669–680 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Serandour, A. A., Brown, G. D., Cohen, J. D. & Carroll, J. S. Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties. Genome Biol. 14, R147 (2013).

Article  PubMed  PubMed Central  Google Scholar 

Giresi, P. G., Kim, J., McDaniell, R. M., Iyer, V. R. & Lieb, J. D. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 17, 877–885 (2007).

Article  CAS  PubMed  Google Scholar 

Amemiya, H. M. et al. Distinct heterochromatin‐like domains promote transcriptional memory and silence parasitic genetic elements in bacteria. EMBO J. 41, e108708 (2022).

Article  CAS  PubMed  Google Scholar 

Rakibova, Y., Dunham, D. T., Seed, K. D. & Freddolino, L. Nucleoid-associated proteins shape the global protein occupancy and transcriptional landscape of a clinical isolate of Vibrio cholerae. mSphere 9, e0001124 (2024).

Article  PubMed  PubMed Central  Google Scholar 

Zeinert, R. D. et al. A legacy role for DNA binding of Lon protects against genotoxic stress. Preprint at bioRxiv https://doi.org/10.1101/317677 (2018).

Ekdahl, A. M. et al. Conserved heterochromatin-like structures with local regulators mediate the iron stress response in mycobacteria. Preprint at bioRxiv https://doi.org/10.1101/2025.08.23.671944 (2025).

Palomar, V. M. et al. Membrane association of active genes organizes the chloroplast nucleoid structure. Proc. Natl Acad. Sci. USA 121, e2309244121 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mihailovic, M. K. et al. Uncovering transcriptional regulators and targets of sRNAs using an integrative data-mining approach: H-NS-regulated RseX as a case study. Front. Cell. Infect. Microbiol. 11, 696533 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ekdahl, A. M. et al. Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs. Nucleic Acids Res. 53, gkaf647 (2025).

Article  PubMed  PubMed Central  Google Scholar 

Trouillon, J., Doubleday, P. F. & Sauer, U. Genomic footprinting uncovers global transcription factor responses to amino acids in Escherichia coli. Cell Syst. 14, 860–871.e4 (2023).

Article  CAS  PubMed  Google Scholar 

Boyle, A. P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311–322 (2008).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schones, D. E. et al. Dynamic regulation of nucleosome positioning in the human genome. Cell 132, 887–898 (2008).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gross, D. S. & Garrard, W. T. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57, 159–197 (1988).

Article  CAS  PubMed  Google Scholar 

Rychel, K. et al. iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning. Nucleic Acids Res. 49, D112–D120 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lempp, M. et al. Systematic identification of metabolites controlling gene expression in E. coli. Nat. Commun. 10, 4463 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Hommais, F. et al. Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS. Mol. Microbiol. 40, 20–36 (2001).

Article  CAS  PubMed  Google Scholar 

Orans, J., Kovach, A. R., Hoff, K. E., Horstmann, N. M. & Brennan, R. G. Crystal structure of an Escherichia coli Hfq Core (residues 2–69)–DNA complex reveals multifunctional nucleic acid binding sites. Nucleic Acids Res. 48, 3987–3997 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Solomon, M. J. & Varshavsky, A. Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures. Proc. Natl Acad. Sci. USA 82, 6470–6474 (1985).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bergendahl, V., Thompson, N. E., Foley, K. M., Olson, B. M. & Burgess, R. R. A cross-reactive polyol-responsive monoclonal antibody useful for isolation of core RNA polymerase from many bacterial species. Protein Expr. Purif. 31, 155–160 (2003).

Article  CAS  PubMed  Google Scholar 

Lacazette, E. A laboratory practical illustrating the use of the ChIP-qPCR method in a robust model: estrogen receptor alpha immunoprecipitation using Mcf-7 culture cells. Biochem. Mol. Biol. Educ. 45, 152–160 (2017).

Article