Fig. 3: Organization of CHINs and CHIDs directed by H-NS and other NAPs.
From: Elementary 3D organization of active and silenced E. coli genome
a, Example contact map with profiles of NAPs distribution, GC content, transcription signal and operon track. b, Distribution of H-NS around CHINs, CHIDs, OPCIDs, inactive operons and active operons. Annotations are consistent with Fig. 2b. c, H-NS motif from the PRODORIC database (left) alongside the CHIN motif identified by HOMER (right). d, A model depicting the organization of a single CHIN, with CHIN length distribution shown (right; n represents the number of CHINs assessed). dsDNA, double-stranded DNA. e, A model illustrating the interaction between two CHINs, where they unfold and fuse to form a stem of a large loop. The distribution of distances at which CHINs interact is also shown (right; n represents the number of CHIN contacts assessed). The boxplots extend from the 25th to 75th percentiles, the whiskers are drawn down to the 10th and up to the 90th percentiles, and the centre line represents the median (d,e). f, Localization of H-NS within the stem regions of CHINs, showing peaks at CHIN stems. g, Number of CHINs overlapping with H-NS peaks. h, Number of HTGs overlapping with CHINs. The P values were calculated using two-sided shuffle test: P < 0.001 (g,h). i–r, Contact maps of two representative CHIN-harbouring regions in WT E. coli cells (i) and the same regions in strains with deletions of the indicated genes (j–n) or in WT cells treated with antibiotics (o–r), illustrating the CHIN reorganization in Δhns cells and complete CHIN disassembly in ΔhnsΔstpA and netropsin-treated cells. The average contact map for CHINs under these conditions is also shown (right).
