Fig. 1 ∣. Accessible chromatin regions in the maize genome.

a, tb1 is expressed in immature inflorescences and silenced in leaves. The genetically mapped tb1 CRE (gray shaded area) displays tissue-dynamic chromatin accessibility and histone modifications. ATAC-seq and ChIP-seq experiments were performed in duplicate and yielded the same results both times. b, Genome-wide distribution of leaf ATAC-seq peaks in relation to the AGPv4.38 annotated genes. gACRs overlap genes; pACRs fall within 2,000 bp of genes; dACRs are > 2,000 bp from genes. c, Lengths of total ATAC-seq peaks. d, Distances of ATAC-seq peaks (excluding gACRs) from the closest annotated gene. e, GC content at each dACR versus gene-distal uniquely mapping negative control regions. f, Percentage of each class of ACR that overlap ≥ 1 DAP-seq TF peaks. g, Meta-analysis of DAP-seq peak signals for individual TFs at dACR summits. No replicates of this analysis were performed. h, Distribution of Arabidopsis-derived TF binding motifs at dACR summits. i, Number of total SNPs among maize inbred lines or j, phenotype-associated SNPs per 10 bp bins flanking dACR summits. For normalization of i and j, the negative control distribution was subtracted from the dACR distribution and the difference was plotted. k, Probability that a cis-eQTL's highest-significance SNP overlaps a dACR. Y-axis shows posterior probability. The center values correspond to the medians of the distributions. Figures e-k use the same set of negative control regions (i.e. uniquely mapping, intergenic, non-accessible regions).