ArticleGenome biology2022
Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed.
- 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
- Article
- Dynamic reorganization of three-dimensional genome architecture during Populus diversification.Nature ecology & evolution · 2026Article
- PlantCTCIP: Chromatin Interaction Prediction Using Convolutional Neural Network and Transformer in Plants.Plant biotechnology journal · 2026Article
- Chromatin accessibility landscape and its association with heterosis in maize hybrids.Nature communications · 2026Article
- NanoLoop: A Deep Learning Framework Leveraging Nanopore Sequencing for Chromatin Loop Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome.Cell genomics · 2026Article
- Domestication shaped the chromatin landscape of grain amaranth.Nature communications · 2025Article
- Conservation and variability of long-range interactions in structurally diverse maize genomes.Nature communications · 2025Article
- Article
- TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation.Science advances · 2025Article
- Chromatin loops gather targets of upstream regulators together for efficient gene transcription regulation during vernalization in wheat.Genome biology · 2024Article
- LOGOWheat: deep learning-based prediction of regulatory effects for noncoding variants in wheats.Briefings in bioinformatics · 2024Article
- Unveiling RNA structure-mediated regulations of RNA stability in wheat.Nature communications · 2024Article
- Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.Molecular biology and evolution · 2024Article
- Mind the gap: Epigenetic regulation of chromatin accessibility in plants.Plant physiology · 2024Review
- Differential editing efficiencies in cereal crops: a comparative analysis of tRNA and ribozyme multiplexed guide delivery.Frontiers in plant science · 2024Article
- Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat.Nature communications · 2023Article
- LHP1-mediated epigenetic buffering of subgenome diversity and defense responses confers genome plasticity and adaptability in allopolyploid wheat.Nature communications · 2023Article
- Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat.Nature communications · 2023Article
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12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBread wheat (Triticum aestivum) is an allohexaploid that is generated by two subsequent allopolyploidization events. The large genome size (16 Gb) and polyploid complexity impede our understanding of how regulatory elements and their interactions shape chromatin structure and gene expression in wheat. The open chromatin enrichment and network Hi-C (OCEAN-C) is a powerful antibody-independent method to detect chromatin interactions between open chromatin regions throughout the genome.
resultsHere we generate open chromatin interaction maps for hexaploid wheat and its tetraploid and diploid relatives using OCEAN-C. The anchors of chromatin loops show high chromatin accessibility and are concomitant with several active histone modifications, with 67% of them interacting with multiple loci. Binding motifs of various transcription factors are significantly enriched in the hubs of open chromatin interactions (HOCIs). The genes linked by HOCIs represent higher expression level and lower coefficient expression variance than the genes linked by other loops, which suggests HOCIs may coordinate co-expression of linked genes. Thousands of interchromosomal loops are identified, while limited interchromosomal loops (0.4%) are identified between homoeologous genes in hexaploid wheat. Moreover, we find structure variations contribute to chromatin interaction divergence of homoeologs and chromatin topology changes between different wheat species. The genes with discrepant chromatin interactions show expression alteration in hexaploid wheat compared with its tetraploid and diploid relatives.
conclusionsOur results reveal open chromatin interactions in different wheat species, which provide new insights into the role of open chromatin interactions in gene expression during the evolution of polyploid wheat.
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