Fig. 2

Characterization of Hi-C chromatin loop anchor and interior regions. a Overlap of replicates 1 and 2 chromatin loops with high-resolution chromatin interactions (see text). Percentages of high-resolution chromatin interactions (Y-axis) mapping with replicates 1 and 2 chromatin loops are shown (anchor-to-anchor, anchor-to-interior, interior-to-interior or not mapping). Numbers within each box indicate counts of high-resolution chromatin interactions for each category. b Overlap of B73 leaf v04 ATAC-Seq peaks and expressed genes (see text) with replicates 1 and 2 chromatin loops. Percentages of peaks and expressed genes overlapping with loop anchors, loop interiors, or not overlapping, are shown (Y-axis). Numbers within each box indicate counts of peaks or expressed genes for each category. c Wilcoxon test plots for gene expression differentials between expressed genes overlapping with replicate 1 loop anchors, overlapping with replicate 1 loop interiors or not overlapping. d Overlap of distinct high-resolution chromatin interaction anchors with Hi-C chromatin loop anchors and interiors. Percentages (Y-axis) of distinct high-resolution anchors mapping to Hi-C loop anchors, interiors, or not overlapping to any Hi-C features are shown for replicates 1 and 2 chromatin loops (respective counts are shown within each box). e High-resolution anchors co-locating with replicates 1 and 2 loop interiors and, from bottom to top, 1) expressed genes flanked by overlapping open chromatin peaks or peaks located <2Kbps away; 2) expressed genes and open chromatin peaks located >2Kbps away from the gene; 3) open chromatin peaks and expressed gene located >2Kbps away from the peak; and 4) no overlapping features (expressed gene or open chromatin peak). Counts are shown for each category