Fig. 2: Contact profile of single, active transcription unit within an entire genome.

a, Hi-C contact maps (bin: 1 kb) of E. coli chromosome carrying a single T7 promoter (green triangle), in absence (left) or presence (right) of rifampicin. Ec RNAP: E. coli RNA Pol II. Top: cells grown in glucose media, when the T7 RNA Pol is not expressed. Middle: cells grown in presence of arabinose, with expression of the T7 RNA Pol. Bottom: log₂ ratio contact maps with and without induction of the T7 promoter. Magnification of the T7 promoter region, represented using Serpentine flexible binning (Methods)⁴⁸. b, Magnification of the T7 promoter in the normalized contact maps, with and without induction and in presence and absence of rifampicin. From left to right: T7 promoter off, no rif; T7 on, no rif; T7 on, + rif. For each window and condition, a schematic representation of the region’s genetic content is presented on the top, with the operons within the 10% most transcribed indicated in blue and red for forwards and reverse orientation, respectively (that is, secDEF and cyoABCD). The corresponding RNA-seq tracks (CPM) are plotted under the maps. In presence of T7 RNA Pol and rifampicin, the numbered labels on the map highlight the features discussed in the text: (1) arched stripe pattern; (2) bundle region. c, Average genome structures using Shrek of the corresponding 2D contact maps of the E. coli bacterial chromosome in the different conditions. The green, red and blue arrows represent the pT7, ori and ter positions, respectively. The 3D representations are not the physical structure of the genome, but the average structure of the population of cells that we observed. d, Modeling of the Hi-C contact maps using the RNA Pol distribution on the genome and using the second model (Methods).