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

Abstract

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.

Regulation of stress-induced inositol metabolism in plants: a phylogenetic search for conserved cis elements

“…In fact, all the isoforms of a single gene may not have similar cis-signatures and/or epigeneticsignatures. This shows the importance of DNA-binding assays and chromatin immunoprecipitation for determining the functional transcription factors active (Wang et al 2021;Kumar et al 2021). The epigenetic landscape determining the inositol metabolism is yet to be explored.…”

ccnWheat: A Database for Comparing Co-expression Networks Analysis of Allohexaploid Wheat and Its Progenitors

“…However, H3K27me3 modification had obvious differences in different tissues and developmental stages, while H3K4me3 did not. Spikelet reduced H3K27me3 peaks carrying the enriched CArG-box motifs have been found in wheat [71]. Taken together, gaining the CArG motif may affect WAPO-A1 functions in regulating the total number of spikelets in AABBDD, though this requires further experimental verification.…”

“…Flower-specific TFs were confirmed function in removing the H3K27me3 surrounding flower-specific regulatory elements in Arabidopsis thaliana [69,70]. In wheat, the enriched CArG-box motifs were found in the spikelet reduced H3K27me3 peaks [71].…”

Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation

“…Genome asymmetry is a common phenomenon observed in interspecific hybrids and allopolyploids, such as cotton, Brassica , and wheat [ 31 , 53 , 54 ]. Subgenome dominance reflects the preference of homoeologous gene expression in different subgenomes [ 55 ].…”