Fig. 2 ∣. Chromatin attributes of dACRs and patterns among dACR-flanking genes.

a, Meta-analysis of DNA methylation, ATAC-seq, ChIP-seq, and RNA-seq signals at transcription start sites (TSS) and termination sites (TTS) of annotated genes, ranked by expression. 2 kb upstream and downstream of TSS and TTS are included. Note that the bottom ~1/3 of ranked genes likely correspond to pseudogenes. b-g, Chromatin attributes at dACRs, aligned at dACR summits and clustered into four groups. Shown are +/− 2 kb from summits. ChIP-seq and RNA-seq experiments for a-g were performed in duplicate and yielded identical results each time. h, GO term enrichment for the nearest genes flanking the dACRs on both sides. p-values were determined with a two-sided hypergeometric test, as implemented in the BiNGO program (see methods). p-values were adjusted for multiple testing with Benjamini & Hochberg. Sample sizes were twice the number of dACRs in each chromatin group (since each dACR had two flanking genes). i, Expression Shannon entropy values and j, expression levels (TPM) of the nearest genes on both sides of each dACR. k, Percent of total leaf dACRs in each chromatin group that are present in leaves but absent from inflorescences (i.e., the leaf dACR does not overlap an inflorescence dACR). l, Among the genes flanking leaf-specific differential dACRs, the percent of first neighbor (primary) and second neighbor (secondary) genes that are differentially expressed, and m, the percent of differentially expressed genes for which the differential dACR occurs downstream or upstream of the gene's 5' end. All figures use the same set of negative control regions. For i, j, l, and m, percentages from genes flanking intergenic negative control regions were subtracted from the percentages of genes flanking dACRs.