Fig. 4: Activation of HTGs on H-NS and double hns stpA knockout.
From: Elementary 3D organization of active and silenced E. coli genome
a–d, Gene expression changes following deletion of hns and stpA (a), exposure to 200 µg ml−1 netropsin (b), deletion of hns (c) and deletion of stpA (d) as determined by RNA sequencing. The distribution of HTGs and non-HTGs that are upregulated, downregulated or insignificantly altered in Δhns, ΔstpA, ΔhnsΔstpA and netropsin-treated E. coli cells is also shown. The P values were calculated using two-sided Wald test and adjusted for multiple testing using Benjamini–Hochberg correction with false discovery rate set to 0.05. FC, fold change. e, Expression levels of genes overlapping with CHINs and those not overlapping with CHINs in WT E. coli cells (green) compared with the expression levels of the same gene groups in Δhns (blue), ΔstpA (white) and ΔhnsΔstpA (red). f, Expression changes of CHIN-associated and CHIN-non-associated genes in response to Δhns, ΔstpA and ΔhnsΔstpA. g,h, Similar to panels e and f, but focusing specifically on HTGs. The number of genes (n) is indicated. The boxplots extend from the 25th to 75th percentiles, whiskers are drawn down to the 10th and up to the 90th percentiles, and the centre lines represent the median. The P values were calculated using the two-sided Kolmogorov–Smirnov test: **P < 0.01 and ****P < 0.0001. The black dashed line indicates the fold change value of 1. i, Changes in expression of selected HTGs upon Δhns, ΔstpA and ΔhnsΔstpA, as determined by RT–qPCR. Signals are normalized to 16S rRNA, with the expression level in WT cells set to 1. Data are presented as mean ± s.d. j, Micro-C contact maps of regions harbouring HTGs selected for RT–qPCR analysis in WT, ΔstpA, Δhns and ΔhnsΔstpA cells. k, Growth rates of WT, ΔstpA, Δhns and ΔhnsΔstpA E. coli cells measured using Bioscreen. Data are presented as mean ± s.d. from n = 7 biological replicates for WT, ΔstpA and Δhns, and n = 14 for ΔhnsΔstpA. OD600, optical density at 600 nm.
