library_construction_protocol: According to the protocol described in Crémazy, F. G., Rashid, F. Z. M., Haycocks, J. R., Lamberte, L. E., Grainger, D. C., & Dame, R. T. (2018). Determination of the 3D genome organization of bacteria using Hi-C. In Bacterial Chromatin (pp. 3-18). Humana Press, New York, NY. Minor modifications were included: the restriction digestion ends of HpaII-digested chromatin was not filled in with biotin-labelled nucleotides, and NGS library preparation was performed directly after reverse cross-linking and library purification (all intervening steps were skipped). KAPA HyperPlus library preparation kit according to the protocol described in Crémazy, F. G., Rashid, F. Z. M., Haycocks, J. R., Lamberte, L. E., Grainger, D. C., & Dame, R. T. (2018). Determination of the 3D genome organization of bacteria using Hi-C. In Bacterial Chromatin (pp. 3-18). Humana Press, New York, NY. Minor modifications were included: biotin-labelled ligation junctions were not present in the library, hence, the step describing the enrichment of biotin-labelled ligation junctions was not performed.