Fig. 1: The bacterial chromosome is structured by tens of small transcriptionally active 3D units.

a, Hi-C normalized contact map of WT E. coli cells (bin: 1 kb). The five yellow squares I–V underline representative 64-kb regions magnified in either b or in Extended Data Fig. 1. b, Magnifications of regions III and V in absence (left) and presence (right) of rifampicin. Ec RNAP: E. coli RNA Pol II. For each window and condition: Top: a schematic representation of the region’s genetic content, with the names of genes within the 10% most transcribed indicated in blue and red for forwards and reverse orientation, respectively, and silent EPODs regions in green²¹. Middle: normalized contact map (bin: 0.5 kb). Bottom: RNA-seq profile in CPM. Plaid-like pattern positions are pointed with greenish rectangles on the maps. c, Venn diagram of EPODs labeled regions²¹ and of regions labeled as bundle domain. The metric used corresponds to the total size of the corresponding regions, in kb. d, Top: pileup of 50 kb contact map windows (bin: 0.5 kb) centered on the start codons (AUG) of the 5% (left) and 10% (right) most transcribed genes of the genome. Bottom: corresponding pileup of transcription (RNA-seq) tracks. Green arrowheads indicate a faint stripe signal extending from the TSS. e, Pileup of 50-kb contact map windows centered on the TSS of the to 10% and 20% most transcribed TUs (that is operons). Bottom: corresponding pileup of transcription (RNA-seq) tracks.