Figure 4

Accessibility dynamics are reflected in histone PTM states and 3D genome organization

(A) Browser shot around the dre-mir-9-5 locus showing strong concordance between (from top to bottom) SHAMAN 3D interaction score heatmap, Cicero co-accessibility arcs for scores >0.28 (top 1% score cutoff; dashed line), histone PTM signals and promoter-like/enhancer-like HMM state calls, cluster-collapsed sci-ATAC-seq signals, sci-ATAC-seq segmentation calls, H3K36me3 signal, and nascent chromatin-associated RNA signal. Co-accessibility arcs are clearly enriched between strong interaction regions (orange/yellow in Hi-C heatmap), and these anchor points are clearly marked with enhancer-like and promoter-like PTMs, as captured by the histone PTM states. Co-accessibility is also observed in the sci-ATAC-seq signal tracks and reflected in the similar coloring of the sci-ATAC-seq segmentation calls.

(B) A heatmap representing histone PTM chromatin states learned. Each state is a multivariate Gaussian distribution and is plotted as the mean scaled ChIP-seq signal for each PTM.

(C) 1-kb segments from the sci-ATAC-seq foreground are classified for their most representative histone PTM state (see STAR Methods), and plotted is the log2 ratio of class occurrence therein compared to class occurrence in all genomic 1-kb bins. The color scale represents the type of histone PTM state as determined from genome-wide frequency and positional enrichment around annotated-TSS proximal and distal segments (Figures S4B–S4D). Stars represent significance from hypergeometric tests for enrichment (for states 1–12, p values are <2.2 × 10⁻¹⁶, <2.2 × 10⁻¹⁶, <2.2 × 10⁻¹⁶, <2.2 × 10⁻¹⁶, 1, <2.2 × 10⁻¹⁶, <2.2 × 10⁻¹⁶, 0.981, 0.00000000641, <2.2 × 10⁻¹⁶, 1, and 1, and n values are 6,223, 12,441, 12,871, 6,873, 6,951, 9,283, 12,875, 10,610, 8,231, 11,249, 8,386, and 46,079).

(D) Entropy scores (low = cell specific, high = constitutive) for foreground sci-ATAC-seq regions were split into deciles, and within each decile the number of regions for each type of histone PTM state was counted and plotted.

(E) In situ Hi-C insulation scores for foreground sci-ATAC-seq regions were split into deciles, and within each decile the number of regions for each type of histone PTM state was counted and plotted.

(F) In situ Hi-C insulation scores for foreground sci-ATAC-seq regions were split into deciles and then split according to their histone PTM type. The entropy score is plotted for the resulting promoter-like histone PTM regions, and the other 3 histone PTM types can be seen in Figure S4I. p value is the result of a Welch’s unpaired t test between the entropy scores for the 1st and 10th insulation deciles with promoter-like chromatin states (mean 4.028477 versus 4.007515, df = 463.39, n = 2,068 and 374, respectively).

(G) SHAMAN Hi-C interaction score means (full plot lines) or distributions (inset boxplots) are plotted for pairs of sci-ATAC-seq foreground regions that are >25-kb apart and within the same TAD. Region pairs are split first by Cicero co-accessibility score percentiles and then by having a promoter-like histone PTM state in one or both of the 2 regions (prom-cont), having no promoter-like histone PTM regions but having 1 or 2 enhancer-like PTM regions (enh-cont), or where neither region is promoter-like or enhancer-like (other). Mean lines for all 100 percentiles are plotted for ease of visualization, and boxplot insets for the 1st, 25th, 50th, 75th, or 100th percentiles are shown to give a better sense of the distributions. Counts for each group can be seen in Figure S4J. Stars represent significance from Welch’s unpaired t tests between the 100th and 75th percentiles (prom-cont: mean 26.62588 versus 9.33010, p < 2.2e−16, df = 2,458.4, n = 1,132 and 1,402; enh-cont: mean 19.87832 versus 10.80246, p < 2.2e−16, df = 7514.1, n = 3,829 and 3,740; other: mean 8.958823 versus 9.253661, p = 0.6012, df = 2201.4, n = 1,156 and 1,079).