Fig. 1

ChIA-PET analysis defines chromatin interactions in Arabidopsis. a Cross-linked chromatin was fragmented, subjected to ChIP enrichment of three types of representative chromatin marks in Arabidopsis, namely transcriptionally active (H3K4me3, RNAPII, and H3K4me1), Polycomb-repressive (H3K27me3), and heterochromatic (H3K9me2), followed by proximity ligation. Deoxyribonucleic acid constructs consisting of two tags from interacting DNA fragments were sequenced. Overlapping regions of inter-ligation paired-end tags (PETs) were used to define chromatin interactions. Anchor peak, a ChIP-seq peak involved in chromatin interaction; basal peak, a ChIP-seq peak not involved in chromatin interaction (see Additional file 2: Table S1 for details). b Examples of DNA FISH-analyzed nuclei. Anchor regions are stained red and green, whereas DNA is stained blue. Bar = 2 µm. c, d Upper: ChIA-PET interaction heatmaps of chromosome 4 at 25 and 10 kb resolution. The graphs are from the combined ChIA-PET data. Lower: A/B compartments. The graphs show the A (green histogram) and B (orange histogram) compartments represented by the first eigenvector from principal component analysis (PCA). e Compartments, and chromatin loops and binding peaks of the indicated factor in the box region of panel (d). The data tracks show A/B compartments, chromatin loops, profiling of representative histone modifications and RNAPII occupancy, and gene transcription. Of the RNA-seq track, the red and black wiggle plots represent forward and reverse strand RNA-seq reads, respectively. f Distribution of the indicated factor-connected interactions among compartments A and B and across A-B