GSE139019
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. Overall design: 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.