Fig. 3

Distinctive and predictive chromatin signatures of functional elements. a Chromatin states determined with a multivariate hidden Markov model. The heatmap presents the emission parameters based on genome-wide combinations of epigenetic marks. Dark blue represents a high frequency of a given mark at regions corresponding to the chromatin state. Each row represents one state, and each column represents one chromatin mark, except the last column, which represents the genomic coverage of the given state. Replicates displayed good consistency. b Bar plot indicating the distribution of genomic positions in each state for various genomic features. c Pie plot presenting the fraction of regions in each chromatin state covering mRNA or lncRNA sequencing reads. d Genomic tracks illustrating three predicted genes based on the signatures of chromatin states 1–4. The first gene was annotated according to the IWGSC RefSeq genome assembly (version 1.0), whereas the other two genes were not annotated, but had a high RNA-seq read density. The data in square brackets represent the range of normalized read densities. The number of reads in each position was normalized against the total number of reads (reads per million mapped reads). e, f For each chromatin state, the fractions of open chromatin regions characterized by DHS read density (e) and conservation score across wheat species (f) were calculated. g Boxplot presenting the distribution of DNA methylation ratios of each chromatin state in three sequence contexts. h Fraction of each chromatin state overlapping with a CpG island. i Number of regions in each chromatin state associated with various types of TEs. j Distribution of TEs in various genomic segments associated with distal (R1 and R3) as well as interstitial and proximal (R2 and C) regions in chromatin states 12 and 13. k Cumulative distances of TEs to the nearest genes in chromatin states 12 and 13