ArticleGenome biology2019
The bread wheat epigenomic map reveals distinct chromatin architectural and evolutionary features of functional genetic elements.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers, 1 of them a synthesis that pooled it.
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Who cites it
82 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic synthesis of CRISPR/Cas applications for enhancing salt tolerance in crops: a decade of progress and challenges.BMC plant biology · 2026Pooled it
- 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
- Genome-Wide Identification of theCurrent issues in molecular biology · 2026Article
- H3K4 Methylation Readers in Plants: Recognition Mechanisms and Biological Functions.International journal of molecular sciences · 2026Review
- Ancient Whole-Genome Duplication and Lineage-Specific Retention Shape the Diversification of bZIP Transcription Factors in Pooideae.Plants (Basel, Switzerland) · 2026Article
- DNA methylation around transcription start sites is not globally associated with transcription in the grain of natural and synthetic hexaploid wheat.BMC plant biology · 2026Article
- Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome.Cell genomics · 2026Article
- Features of DNA methylome in Capsicum spp.Epigenetics & chromatin · 2025Article
- Precise control of chromatin loop extrusion enhances sustainable green revolution yield in rice.Nature genetics · 2025Article
- Review
- Transposable elements drive the subgenomic divergence of homoeologous genes to shape wheat domestication and improvement.Plant communications · 2025Article
- TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation.Science advances · 2025Article
- Epigenome profiling reveals distinctive regulatory features and cis-regulatory elements in pepper.Genome biology · 2025Article
- Centromere-size reduction and chromatin state dynamics following intergenomic hybridization in cotton.PLoS genetics · 2025Article
- Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects.International journal of molecular sciences · 2025Review
- EGDB: A comprehensive multi-omics database for energy grasses and the epigenomic atlas of pearl millet.iMeta · 2025Article
- Epigenomic and 3D genomic mapping reveals developmental dynamics and subgenomic asymmetry of transcriptional regulatory architecture in allotetraploid cotton.Nature communications · 2024Article
- Chromatin loops gather targets of upstream regulators together for efficient gene transcription regulation during vernalization in wheat.Genome biology · 2024Article
- Genome-wide mapping of main histone modifications and coordination regulation of metabolic genes under salt stress in pea (Horticulture research · 2024Article
22 more citing papers are in PubMed but not listed here.
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13 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundBread wheat is an allohexaploid species with a 16-Gb genome that has large intergenic regions, which presents a big challenge for pinpointing regulatory elements and further revealing the transcriptional regulatory mechanisms. Chromatin profiling to characterize the combinatorial patterns of chromatin signatures is a powerful means to detect functional elements and clarify regulatory activities in human studies.
resultsIn the present study, through comprehensive analyses of the open chromatin, DNA methylome, seven major chromatin marks, and transcriptomic data generated for seedlings of allohexaploid wheat, we detected distinct chromatin architectural features surrounding various functional elements, including genes, promoters, enhancer-like elements, and transposons. Thousands of new genic regions and cis-regulatory elements are identified based on the combinatorial pattern of chromatin features. Roughly 1.5% of the genome encodes a subset of active regulatory elements, including promoters and enhancer-like elements, which are characterized by a high degree of chromatin openness and histone acetylation, an abundance of CpG islands, and low DNA methylation levels. A comparison across sub-genomes reveals that evolutionary selection on gene regulation is targeted at the sequence and chromatin feature levels. The divergent enrichment of cis-elements between enhancer-like sequences and promoters implies these functional elements are targeted by different transcription factors.
conclusionsWe herein present a systematic epigenomic map for the annotation of cis-regulatory elements in the bread wheat genome, which provides new insights into the connections between chromatin modifications and cis-regulatory activities in allohexaploid wheat.
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