ArticlePlant physiology2016
Histone Modifications Define Expression Bias of Homoeologous Genomes in Allotetraploid Cotton.
Article in Plant physiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 53 citations in OpenAlex.
- Comparative Analysis of Floral Transcriptomes inPlants (Basel, Switzerland) · 2025Article
- A Genome-Wide Alternative Splicing Analysis ofPlants (Basel, Switzerland) · 2024Article
- Translational Regulation of Duplicated Gene Expression Evolution in Allopolyploid Cotton.Genes · 2024Article
- Genome evolution of the ancient hexaploidProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton.Molecular biology and evolution · 2024Article
- Epigenetic Regulation of Subgenomic Gene Expression in AllotetraploidPlants (Basel, Switzerland) · 2023Article
- Comprehensive transcriptional variability analysis reveals gene networks regulating seed oil content of Brassica napus.Genome biology · 2022Article
- Asymmetric subgenomic chromatin architecture impacts on gene expression in resynthesized and natural allopolyploid Brassica napus.Communications biology · 2022Article
- Expression Level Dominance and Homeolog Expression Bias Upon Cold Stress in the F1 Hybrid Between the InvasiveFrontiers in genetics · 2022Article
- Multi-Dimensional Molecular Regulation of Trichome Development inFrontiers in plant science · 2022Review
- Conservation and trans-regulation of histone modification in the A and B subgenomes of polyploid wheat during domestication and ploidy transition.BMC biology · 2021Article
- Profiling of H3K4me3 and H3K27me3 and Their Roles in Gene Subfunctionalization in Allotetraploid Cotton.Frontiers in plant science · 2021Article
- Refinement of bamboo genome annotations through integrative analyses of transcriptomic and epigenomic data.Computational and structural biotechnology journal · 2021Article
- Dynamic and reversible DNA methylation changes induced by genome separation and merger of polyploid wheat.BMC biology · 2020Article
- Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement.Nature genetics · 2020Article
- Genome-wide identification of histone methylation (H3K9BMC genomics · 2019Article
- Epigenetic perspectives on the evolution and domestication of polyploid plant and crops.Current opinion in plant biology · 2018Review
- PCSD: a plant chromatin state database.Nucleic acids research · 2018Article
- Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid.Genome biology · 2017Article
- Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation.Scientific reports · 2017Article
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Authors and funding
6 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Histone modifications regulate gene expression in eukaryotes, but their roles in gene expression changes in interspecific hybrids or allotetraploids are poorly understood. Histone modifications can be mapped by immunostaining of metaphase chromosomes at the single cell level and/or by chromatin immunoprecipitation-sequencing (ChIP-seq) for analyzing individual genes. Here, we comparatively analyzed immunostained metaphase chromosomes and ChIP-seq of individual genes, which revealed a chromatin basis for biased homoeologous gene expression in polyploids. We examined H3K4me3 density and transcriptome maps in root-tip cells of allotetraploid cotton (Gossypium hirsutum). The overall H3K4me3 levels were relatively equal between A and D chromosomes, which were consistent with equal numbers of expressed genes between the two subgenomes. However, intensities per chromosomal area were nearly twice as high in the D homeologs as in the A homeologs. Consistent with the cytological observation, ChIP-seq analysis showed that more D homeologs with biased H3K4me3 levels than A homeologs with biased modifications correlated with the greater number of the genes with D-biased expression than that with A-biased expression in most homeologous chromosome pairs. Two chromosomes displayed different expression levels compared with other chromosomes, which correlate with known translocations and may affect the local chromatin structure and expression levels for the genes involved. This example of genome-wide histone modifications that determine expression bias of homeologous genes in allopolyploids provides a molecular basis for the evolution and domestication of polyploid species, including many important crops.
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