Fig. 3

Reprogramming of histone modifications during wheat embryogenesis. a Emission probabilities for histone modifications in 12 ChromHMM states, which could be mainly categorized into five groups: Pr (promoter), EnL (enhancer-like), Tr (transcription), PcG (polycomb group), and Hc (heterochromatin) state. The abbreviation following dash: A, active; W, weak; P, poised; S, strong; I, initiation; E, elongation; H, H3K9me2-associated; Ns, No signal. b Heatmap showing the histone modification level at different chromatin states. RPKM was used for data normalization. c Chromatin states transition among different developmental stages. d Percentage of changed chromatin state coverage to the total genome size among different embryonic stages. Colors filled represent the five major chromatin state groups as shown in a. e Dynamic of five major chromatin states during different embryonic stages. Fisher’s Least Significant Difference (LSD) was used for significance calling. f Histone modification dynamic in promoter and genic regions during wheat embryogenesis. g Comparisons of histone modifications H3K27ac, H3K4me3, H3K27me3, and H3K9me3 of collinear regions between Chr. 5A and Chr. 5B. Downregulated (Dn) and upregulated (Up) loci were defined by the log2 (fold change Chr. 5B/ Chr. 5A) values bigger and lower than 1 and − 1, respectively. Nc indicates no change. Color bars and grey lines indicate the chromosome segments and centromere regions as those in Fig. 2d. h Schematic represents the chromatin state dynamic during wheat embryogenesis. The dark and light colors represent the strength and weakness of the signal, respectively