Fig. 4

Ligand-induced enhancement of chromatin contacts within P300 interaction subdomains. a Bar plot depicting the percentage of induced P300 peaks in the P300 hubs with at least five P300 peaks. b P300 local concentration at all P300 interaction subdomains that are ordered based on average P300 density (x-axis) and ligand-induced change in P300 concentration (y-axis). Sub-domains harboring at least five P300 distal binding sites (DBS) are presented. c Total number of chromatin interactions detected at each interaction subdomain upon vehicle dimethyl sulfoxide (DMSO, blue dots) and triamcinolone acetonide (TA) + tumor necrosis factor alpha (TNFα, red dots) treatment is presented. Sub-domains that show no more than 25 % change in total P300 concentration (reads per kilobase per million mapped reads) that either harbor at least one induced P300 DBS (upper panel) and only constitutive P300 DBS (lower panel) are used. p-values (Mann–Whitney) were generated by comparing interaction ratios (TA + TNFα/DMSO) between the induced and constitutive subdomains that are within each bin (shaded area). d Proportion of DBSs to nearest first gene promoters or DBSs to distal gene promoter interactions identified by P300 and RNA polymerase II (POLII) ChIA-PET analysis. TSS transcription start site. e Co-activation-dependent changes in expression of genes that are directly looped to P300 DBSs. P300 DBSs were initially ordered according to agonist-induced P300 recruitment (low to high) and subsequently divided into 10 equal bins. The average transcriptional change of genes in each bin is presented. Expression of genes that are in bins harboring significantly repressed (gray), induced (red), and constitutive (blue) P300 DBSs upon co-stimulation. f Co-activation-induced changes in expression of genes that are within interaction subdomains harboring either induced or only constitutive P300 DBSs