(A) Comparative analysis of global transcriptional responses, comparing up- or down-regulated genes in Ec-hmfA (versus Ec-hmfAnb) to other perturbations (underlying data provided as Figure 7A – source data). Perturbations with high similarity to Ec-hmfA versus Ec-hmfAnb along at least one dimension are highlighted and coloured according to the nature of the perturbation. Values < 0 indicate overall dissimilarity, equivalent to a negative correlation coefficient between the transcriptional responses. Note that the absolute similarity values here have no intrinsic meaning; only the relative distance from the maximum, hmfA/hmfAnb (expo), is meaningful. Note also that similarity should only be interpreted in reference hmfA/hmfAnb (expo). Points labelled ‘exponential phase’ constitute rare cases where, in the original study, differential expression was assessed as expo/stat rather than the more common stat/expo. When flipped, these fall into or close to the pink cluster of stationary phase datasets. (B) Genes controlled by RpoS (identified by comparing the response to isoleucine starvation in WT and ΔrpoS cells, upper panel) are upregulated upon isoleucin starvation but also in histone-expressing strains (illustrated for Ec-hmfA in the lower panel). Based on GSE11087 as provided in GenexpDB. (C) Correspondence between transcriptomic changes in Ec-hmfB versus Ec-hmfBnb and a Δh-ns strain (GSE123554). Direct H-NS targets, as inferred by Gawade et al. (2019), are highlighted in green. (D) Histone occupancy in regions previously found to be bound or unbound by a particular nucleoid-associated protein in E. coli. ∆ histone occupancy is defined as the difference in histone occupancy in a region bound by a given NAP and the nearest unbound region downstream. Negative ∆(histone occupancy) values therefore indicate greater histone occupancy in areas not bound by the focal NAP, suggestive of competition for binding or divergent binding preferences. *p<0.005 **p<0.001.