Fig. 1

Genome-wide mapping of chromatin accessibility in early tassel and ear primordia. a Genome-wide visualization of MNase HS in tassel and ear and aligned against other genomic features: a - Chromosome ideograms; black bars indicate centromeres, b - Repeat elements, c - Gene density, d - Density of conserved non-coding sequences (CNSs), e - Differential nuclease sensitivity (DNS) from tassel, f - DNS from ear, g - DNS from seedling shoot, h - Density of small fragments (< 131 bp) from the light MNase digest (LCS) in tassel, i - LCS in ear, j - Density of gene expression from RNA-seq in 1–2 mm tassel primordia, k - Density of gene expression from RNA-seq in 1–2 mm ear primordia. A 60 kb slice on chromosome 2 is represented in a genome browser view below and includes the liguleless 1 gene and a prominent HS region approximately 20 kb upstream. b The venn diagram compares the portion of MNase HS genome (in Megabases) based on DNS in tassel, ear and shoot tissues. c Distribution of MNase HS sites (based on peak midpoint) across eight genomic features relative to protein coding genes: within 1 and 2 kb upstream of the TSS, the proximal promoter defined as 1 kb upstream and 200 bp downstream of the TSS, 5′ UTR, exon, intron, 3′ UTR, within 1 kb downstream of the TTS, intergenic. Density of DNS signatures were normalized per 10 kb of genomic space per feature. In both tassel and ear, the promoter and 3′ regions of genes are most accessible. d Distribution of distances (in the range of 50 kb) from the midpoints of intergenic MNase HS sites to the closest protein coding gene in ear and tassel. The gray bar plots the distribution of midpoints of genomic space between any two sequential genes in the genome