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Fig. 4 | Genome Biology

Fig. 4

From: 3D genome architecture coordinates trans and cis regulation of differentially expressed ear and tassel genes in maize

Fig. 4

Characterization of TADs and loops and the identification of dOCR-gene loops in ear and tassel. a A representative chromatin interaction map of chromosome 1 in ear and tassel. The arrowheads mark several obvious loops. b Number of TAD boundaries and tissue-specific TAD boundaries identified in ear and tassel. c A case of TAD boundary difference (the boundary is visible only in ear) showing the change in expression of a gene at the boundary (gray shading). The chromatin interaction maps are marked in blue for ear and red for tassel. A DNA motif recognized by TCP TFs is significantly enriched in the TAD boundaries. d Number of chromatin loops with different interaction distances in ear and tassel. e Obvious chromatin loops (> 2 Mb interaction distance) marked in blue boxes are visible on chromosome 3 in ear. Relevant genes and loop connections are shown above the heatmap. f The correlation between gene expression level and the number of loops in ear. g Numbers of gene-gene, intergenic-gene, and intergenic-intergenic loops detected in ear and tassel. h The expression correlation of gene pairs with real loops is significantly higher than that of randomly selected gene pairs with similar interaction distances (p < 2e−16 in both ear and tassel, two-tailed t test). PCC, Pearson correlation coefficient. i, j The average epigenetic features of gene-gene loops showing that highly expressed genes have higher chromatin accessibility together with their looped regions than non-expressed genes in ear (i). The intergenic-gene loops have a similar tendency (j). Highly expressed genes: FPKM > 100; non-expressed genes: FPKM < 1. The target genes and their looped regions are on the left and right sides of the loops, respectively, in the diagram. Only loops with a distance < 500 kb are included. The Wilcoxon test was used to test significance. k, l An example of a highly expressed gene, KN1, which exhibits active co-modifications with its looped gene and intergenic regions in ear (k). In contrast, a non-expressed gene WRKY99 exhibits repressive co-modifications with its looped gene and intergenic regions in ear (l). Gray shadings mark looped regions, and correlated loops in heatmaps are marked with blue circles. m Number of total intergenic anchors of loops that overlap with dOCRs in ear and tassel. Control: the same number of distal regions as dOCRs generated by randomly shifting dOCRs. n Genes that are looped with dOCRs are significantly more highly expressed than those looped with other regions or without loops. The Wilcoxon test was used to test significance. o Examples of four key inflorescence regulation genes involved in chromatin loops (blue boxes) in ear. Gene loci are marked with black dots

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