ArticleGenome biology2020
Differential chromatin accessibility landscape reveals structural and functional features of the allopolyploid wheat chromosomes.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed, 66 citations in OpenAlex.
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- HebQTLs reveal intra-subgenome regulation inducing unbalanced expression and function among bread wheat homoeologs.Genome biology · 2025Article
- ISDH-seq: a robust methodology for profiling and characterization of open chromatin.Plant biotechnology journal · 2025Article
- Rapid reprogramming and stabilization of homoeolog expression bias in hexaploid wheat biparental populations.Genome biology · 2025Article
- The role of DNA content in shaping chromatin architecture and gene expression.The Plant journal : for cell and molecular biology · 2025Article
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- LOGOWheat: deep learning-based prediction of regulatory effects for noncoding variants in wheats.Briefings in bioinformatics · 2024Article
- Functional Characterization of Accessible Chromatin in Common Wheat.International journal of molecular sciences · 2024Article
- Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.Molecular biology and evolution · 2024Article
- DNA Methylation and Chromatin Accessibility Impact Subgenome Expression Dominance in the Common Carp (International journal of molecular sciences · 2024Article
- Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features.Communications biology · 2024Article
- 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
- Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits.Communications biology · 2023Article
- Centromere repositioning and shifts in wheat evolution.Plant communications · 2023Article
- Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei.BMC plant biology · 2023Article
- Transcriptome and Proteome Analysis Revealed the Influence of High-Molecular-Weight Glutenin Subunits (HMW-GSs) Deficiency on Expression of Storage Substances and the Potential Regulatory Mechanism of HMW-GSs.Foods (Basel, Switzerland) · 2023Article
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Authors and funding
5 authors at 2 institutions in 1 country.
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Abstract
backgroundOur understanding of how the complexity of the wheat genome influences the distribution of chromatin states along the homoeologous chromosomes is limited. Using a differential nuclease sensitivity assay, we investigate the chromatin states of the coding and repetitive regions of the allopolyploid wheat genome.
resultsAlthough open chromatin is found to be significantly enriched around genes, the majority of MNase-sensitive regions are located within transposable elements (TEs). Chromatin of the smaller D genome is more accessible than that of the larger A and B genomes. Chromatin states of different TEs vary among families and are influenced by the TEs' chromosomal position and proximity to genes. While the chromatin accessibility of genes is influenced by proximity to TEs, and not by their position on the chromosomes, we observe a negative chromatin accessibility gradient along the telomere-centromere axis in the intergenic regions, positively correlated with the distance between genes. Both gene expression levels and homoeologous gene expression bias are correlated with chromatin accessibility in promoter regions. The differential nuclease sensitivity assay accurately predicts previously detected centromere locations. SNPs located within more accessible chromatin explain a higher proportion of genetic variance for a number of agronomic traits than SNPs located within more closed chromatin.
conclusionsChromatin states in the wheat genome are shaped by the interplay of repetitive and gene-encoding regions that are predictive of the functional and structural organization of chromosomes, providing a powerful framework for detecting genomic features involved in gene regulation and prioritizing genomic variation to explain phenotypes.
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