ArticleThe Plant cell2021
An atlas of wheat epigenetic regulatory elements reveals subgenome divergence in the regulation of development and stress responses.
Article in The Plant cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 93 citations in OpenAlex.
- Integration of the D-Genome Reshapes Gene Transcription, Chromatin Architecture, and Metabolome of Allohexaploid Wheat, Leading to Enhanced Environmental Adaptability.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Transposable element-driven expansion of enhancer RNA repertoires underlies regulatory innovation and polyploid adaptation in cereal crops.Plant communications · 2026Article
- Genomic Expansion and Subgenome Expression Divergence of Sugar Transporters During Polyploid Evolution of Bamboos.Biology · 2026Article
- Genome-Wide Identification of theCurrent issues in molecular biology · 2026Article
- Single-Cell CRISPR: An Efficient Strategy for Decoding Plant Cis-Regulatory Complexity.Plant biotechnology journal · 2026Review
- Dynamics of H3K4me3 and H3K36me3 histone modifications in response to powdery mildew infection in common wheat.BMC plant biology · 2026Article
- The landscape of cotton DNA methylation and its epigenetic regulation in Verticillium wilt resistance.Plant cell reports · 2026Article
- Profiling the transcriptional regulatory network reveals putative shared regulatory elements within homoeologs in polyploid Brassica napus.Genome biology · 2026Article
- The GATA8-GRF5-XTH9 feed-forward loop regulates cell size in poplar.Horticulture research · 2026Article
- Spatial Transcriptomics of Developing Wheat Seed Reveals Concentric Gene Expression Zones and Subgenome Biased Expression of Key Genes.Plant biotechnology journal · 2025Article
- Precise control of chromatin loop extrusion enhances sustainable green revolution yield in rice.Nature genetics · 2025Article
- A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus.BMC genomics · 2025Article
- Comprehensive analysis of bHLH genes in wheat and functional characterization of TabHLH319 in salt tolerance.Plant cell reports · 2025Article
- HebQTLs reveal intra-subgenome regulation inducing unbalanced expression and function among bread wheat homoeologs.Genome biology · 2025Article
- Transposable elements drive the subgenomic divergence of homoeologous genes to shape wheat domestication and improvement.Plant communications · 2025Article
- Epigenetics in the modern era of crop improvements.Science China. Life sciences · 2025Review
- Epigenome profiling reveals distinctive regulatory features and cis-regulatory elements in pepper.Genome biology · 2025Article
- Genome-wide identification and analysis of the WRKY gene family in Sainfoin (Onobrychis viciifolia) and their response to drought, salt, and alkali stress.BMC genomics · 2025Article
- Spatiotemporal transcriptomics reveals key gene regulation for grain yield and quality in wheat.Genome biology · 2025Article
- Time-course transcriptome analysis reveals gene co-expression networks and transposable element responses to cold stress in cotton.BMC genomics · 2025Article
Corrections and comments
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Authors and funding
15 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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 is 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, and demonstrated the coordinated interplay between epiRE sequence contexts, epigenetic factors, and transcription factors in regulating subgenome divergent transcriptional responses to external changes. Together, 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.
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