Fig. 2: Transcription-driven OPCIDs on active operons and transcription-independent CHINs and CHIDs in repressed genomic regions.

a, Average contact map for operons grouped by transcription activity, based on the Red-C signal. b, Transcription level around CHINs, CHIDs, OPCIDs, inactive operons (zero Red-C signal) and active operons (top 10% by Red-C signal). The curves above the piles-up represent median signal, and the shaded areas denote the bootstrap standard error. c, Transcription level within specified genomic features, normalized by feature length. Solid and dashed lines represent the median and 25th to 75th percentiles, respectively. d, Contact maps for a region harbouring the heat shock (HS) operon clpX-lon in normal and HS conditions. e, Average contact maps for σ³² operons under normal and HS conditions. n = 26. f, Schematic illustrating the assembly of an operon into OPCID on transcription activation under HS conditions. g, Frequency of promoter–terminator contacts for operons grouped by Red-C signal into non-transcribed (zero Red-C signal), lowly transcribed (bottom 50% excluding zero), moderately transcribed (50–90%) and highly transcribed (top 10%). n represents the number of operons in each group. Also shown is the frequency of contacts between internal operon regions: one located 20% downstream of the TSS and another 20% upstream of the TES. The boxplots extend from the 25th to 75th percentiles, whiskers are drawn down to the 10th and up to the 90th percentiles, and centre lines represent the median. The P values were calculated using one-way analysis of variance followed by Tukey’s multiple comparisons test. **P < 0.01 and ****P < 0.0001. Exp, expected; NS, not significant; obs, observed. The dashed line indicates the obs/exp contact frequency level of 1. h, Correlation between operon transcription level and the frequency of promoter–terminator contacts. The black line shows linear regression, and the shaded area denotes 95% CI. i, Contact maps for two representative regions harbouring an OPCID and CHINs, shown before and after treatment with 25 µg ml⁻¹ or 750 µg ml⁻¹ Rif. j, Average contact maps for OPCIDs, CHINs and CHIDs before and after exposure to low (25 µg ml⁻¹) or high (750 µg ml⁻¹) concentrations of Rif, illustrating the effect of transcriptional inhibition on these genomic structures.

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