Fig. 3
From: Chromatin loop anchors contain core structural components of the gene expression machinery in maize
Domain-dependent co-location analysis of Hi-C chromatin loops with expression features (open chromatin, expressed genes and eQTL traits) overlapping with at least one of their anchors (a-c). Domain-dependent correlation analysis with gene expression (d). “Inter”: loop span multiple domains with anchors located in distinct domains; “Intra”: loops are fully embedded within a single domain or sub-domain; “1–2 overlap”: loops are contained within one domain or sub-domain, with one or both anchors overlapping with domain or sub-domain boundaries. Percentages of loops from each type co-locating with expression features are shown on the Y-axis. Respective absolute counts are listed within each box. a Co-location of Hi-C replicate 1 and 2 chromatin loops in relation to their overlap with open chromatin regions. b Co--location of Hi-C replicate 1 and 2 chromatin loops in relation to their overlap with expressed genes. c Co--location of Hi-C replicate 1 and 2 chromatin loops in relation to their overlap with eQTL-associated traits. d Gene overlap with chromatin loops and domain types are shown for Hi-C replicate 2 only. (Y-axis) Gene expression levels (computed by averaging TPM counts for four biological replicates). Mean TPM counts: 35.121 (Intra); 37.567 (1–2 overlap); 38.189 (Inter)