Fig. 1

Interaction matrices of maize leaf v04 Hi-C replicate 1 library. a Genome-wide interaction matrix. Each interaction is represented by a “pixel” on the map and the frequency of interactions within a particular region is proportional to the number of pixels. Chromosomes are labeled by numbers (1 to 10, starting with Chr10 at the top left). b Interaction matrix for Chr01. TAD-like chromatin domains and nested sub-domains are marked by squared areas indicating a higher frequency of interactions within a particular chromosomal region. Axis labels indicate coordinates in Mbps. c Interaction matrix for a ~ 3Mbps region located on Chr03. The Hi-C contact matrix shows evidence of domains, with increased cis-interactions at their borders, suggesting the formation of chromatin loops. Seven chromatin loops, marked by solid arrows on both side of the diagonal, are shown as examples. d Distribution of chromatin loop lengths (e.g., distance between anchors) for replicate 1 and replicate 2 Hi-C datasets. Lengths are shown in Kbps (x-axis). The origin of the size oscillation pattern shown for replicate 1 remains to be determined. e Repeat density analysis in anchor and loop interior regions for all loops detected in replicate 1 and replicate 2. Each dot in the graph represents an individual loop. X-axis: fraction of bases within whole anchor regions (0 to 1) that are occupied by conserved elements; Y-axis: fraction of bases within whole interior regions (0 to 1) that are occupied by conserved elements