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Fig. 6 | Genome Biology

Fig. 6

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

Fig. 6

Intergenic SNPs tend to locate in dOCRs and connect with their target genes by intergenic-gene loops. a, b The average distribution of chromatin accessibility (ATAC-seq), histone modifications (a), and DNA methylation (CG, CHG, CHH) levels (b) centered at trait-associated distal SNPs in ear. c Percentages of intergenic SNPs that overlap with dOCRs. Control uses the same number of distal regions as dOCRs by randomly shifting dOCRs. In total, 49,117 intergenic SNPs were used for the calculation for a–c. d A flowering time SNP (DTA, days to anthesis) adjacent to one dOCR interacts with two genes, TE1 and GAP, through loops. e A proposed model showing the chromatin folding comprising TE1, GAP, and dOCRs. The TE1 and GAP genes are marked in blue, and dOCRs are marked in red. dOCR1 is closer to TE1 and GAP than dOCR2, based on the stronger chromatin interaction intensities. f An ear length (EL) SNP interacting with its multiple potential target genes. Gray shadings mark the genome regions involved in loops, and the blue circles mark trait-associated SNPs (d, f)

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