Fig. 2

A putative role of enhancer transcription in regulating subgenome-divergent gene expression and conservation of eRNA regions. a–d Boxplots showing transcript levels of target genes. a Genes associated with transcribed enhancer(s) display higher expression levels. b The enhancer transcriptional level positively correlates with its target gene expression. c The number of associated transcribed enhancers positively correlates with its target gene expression. d Genes targeted by unidirectional or bidirectional enhancers show no significant differences in expression levels. e The enhancer activity (relative intensity) determined in wheat protoplasts of transcribed and untranscribed enhancer candidates. f Correlations between the enhancer activity and the nascent RNA-seq, DHS, and ChIP-seq read density in predicted enhancer regions. g Schematic illustration of the biased expression homeolog genes targeted by enhancers with different transcription levels. Histone modification correlations and physical interactions between enhancers and putative target genes were counted. h Snapshot of a triad (PR10) with subgenome-biased expression and eRNAs. i Subgenome biased transcribed enhancers are enriched with unbalanced expressed homoeologs between each two subgenome pairs (from pNET-seq data). Each dot represents a gene pair in which one homeolog is associated with at least one transcribed enhancer in the same chromosome, while the other homeolog is not. The X-axis and Y-axis coordinates represent the expression levels of the two homeolog genes respectively. Red dots represent gene pairs in which the expression level of a homeolog gene associated with transcribed enhancer(s) was significantly higher than that of the other one not associated with transcribed enhancer; while the grey dots represent a homeolog gene associated with transcribed enhancer(s) was equally or lower expressed than the other one. “A w/ transcribed enhancer, B w/o transcribed enhancer” means homeolog A is associated with transcribed enhancer(s), but homeolog B is not. The odds ratio (OR) is a ratio of two sets of odds to measure the degree to which homeolog gene expression is correlated with its association with enhancer(s). See detailed analyses and interpretation in Additional file 1: Figure S15. j Merge all homoeolog pairs in i showed that the dominantly expressed homoeologs essentially associated with transcribed enhancers. k, l Nucleotide diversity distribution of enhancers with eRNA and random intergenic regions across the genome (k) and within A, B, and D subgenomes (l)