An atlas of wheat epigenetic regulatory elements reveals subgenome-divergence in the regulation of development and stress responses

Wheat (Triticum aestivum) has a large allohexaploid genome. Subgenome-divergent regulation contributed to genome plasticity and the domestication of polyploid wheat. However, the specificity encoded in the wheat genome determining subgenome-divergent spatio-temporal regulation has been largely unexplored. The considerable size and complexity of the genome are major obstacles to dissecting the regulatory specificity. Here, we compared the epigenomes and transcriptomes from a large set of samples under diverse developmental and environmental conditions. Thousands of distal epigenetic regulatory elements (distal-epiREs) were specifically linked to their target promoters with coordinated epigenomic changes. We revealed that subgenome-divergent activity of homologous regulatory elements are affected by specific epigenetic signatures. Subgenome-divergent epiRE regulation of tissue specificity is associated with dynamic modulation of H3K27me3 mediated by Polycomb complex and demethylases. Furthermore, quantitative epigenomic approaches detected key stress responsive cis- and trans-acting factors validated by DNA Affinity Purification and sequencing (DAP-seq), and demonstrated the coordinated interplay between epiRE sequence contexts, epigenetic factors, and transcription factors in regulating subgenome divergent transcriptional responses to external changes. Thus, this study provides a wealth of resources for elucidating the epiRE regulomics and subgenome-divergent regulation in hexaploid wheat, and gives new clues for interpreting genetic and epigenetic interplay in regulating the benefits of polyploid wheat. To systematically characterize RE repertoire of bread wheat, their dynamic regulatory landscape as well as the interplay between REs, we obtained the chromatin activity for a total of 7 typical tissues and 8 external stimuli in bread wheat by performing chromatin immunoprecipitation coupled to massively parallel DNA sequencing (ChIP-seq) for three well-studied histone modifications known to reliably capture enhancer and promoter activities, including acetylated histone 3 at lysine 9 (H3K9ac) and tri-methylated histone 3 at lysine 4 (H3K4me3) associated with active regulatory regions, and tri-methylated histone 3 at lysine 27 (H3K27me3) associated with Polycomb repressed regions, together with gene expression profiles across 15 samples.