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Focusing on the DNA-bridging nucleoid proteins Fis and H-NS, and integratingseveral independent experimental and bioinformatic data sources, we investigatethe links between chromosomal spatial organization and global transcriptionalregulation. By means of a novel multi-scale spatial aggregation analysis, weuncover the existence of contiguous clusters of nucleoid-perturbation sensitivegenes along the genome, whose expression is affected by a combination oftopological DNA state and nucleoid-shaping protein occupancy. The clusterscorrelate well with the macrodomain structure of the genome. The mostsignificant of them lay symmetrically at the edges of the ter macrodomain andinvolve all of the flagellar and chemotaxis machinery, in addition to keyregulators of biofilm formation, suggesting that the regulation of the physicalstate of the chromosome by the nucleoid proteins plays an important role incoordinating the transcriptional response leading to the switch between amotile and a biofilm lifestyle.

Gene clusters reflecting macrodomain structure respond to nucleoid perturbations