Fig. 3

HMGN proteins bind to promoter interaction Regions (PIRs), which are highly enriched for cis-regulatory features involved in active transcription. A Chromatin features of promoter-interacting fragments detected with CHiCAGO. Yellow bars indicate overlaps of the genomic features with cis-interacting fragments within 1 Mb of promoter baits; blue bars indicate expected overlap values based on 100 random subsets of HindIII fragments. These subsets were selected to have a similar distribution of distances from gene promoters as the interacting fragments. Error bars represent 95% confidence intervals. Genomic features include ChIP-seq peaks of HMGN1/2, histone markers, CTCF, and p300. The difference between detected interactions and the expected value is significant for all genomic features with p value < 1e⁻³⁰. The features involved in positive transcription regulation have a fold enrichment of ~ 2–3 while the repressive markers, H3K27me3 and H3K9me3, are either only slightly enriched or depleted. B Upper panel: snapshots of interactions with the Erc2 promoter identified with CHiCAGO in MEF cells. Lower panel: ChIP-seq signals of HMGN1, HMGN2 and H3K27ac in the same region. HMGN proteins specifically occupy at MEFs-specific site (Erc2) and its enhancers in MEF cells