The Plant Cell
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.
| 论文编号: | DOI:10.1093/plcell/koab028 |
| 论文题目: | An Atlas of Wheat Epigenetic Regulatory Elements Reveals Subgenome Divergence in the Regulation of Development and Stress Responses |
| 英文论文题目: | An Atlas of Wheat Epigenetic Regulatory Elements Reveals Subgenome Divergence in the Regulation of Development and Stress Responses |
| 第一作者: | Meiyue Wang, Zijuan Li, Yu’e Zhang, Yuyun Zhang, Yilin Xie, Luhuan Ye, Yili Zhuang, Kande Lin, Fei Zhao, Jingyu Guo, Wan Teng, Wenli Zhang, Yiping Tong, Yongbiao Xue, Yijing Zhang |
| 英文第一作者: | Meiyue Wang, Zijuan Li, Yu’e Zhang, Yuyun Zhang, Yilin Xie, Luhuan Ye, Yili Zhuang, Kande Lin, Fei Zhao, Jingyu Guo, Wan Teng, Wenli Zhang, Yiping Tong, Yongbiao Xue, Yijing Zhang |
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| 发表年度: | 2021-06-02 |
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| 摘要: | 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. |
| 英文摘要: | 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. |
| 刊物名称: | The Plant Cell |
| 英文刊物名称: | The Plant Cell |
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| 其它备注: | Meiyue Wang, Zijuan Li, Yu’e Zhang, Yuyun Zhang, Yilin Xie, Luhuan Ye, Yili Zhuang, Kande Lin, Fei Zhao, Jingyu Guo, Wan Teng, Wenli Zhang, Yiping Tong, Yongbiao Xue, Yijing Zhang. An Atlas of Wheat Epigenetic Regulatory Elements Reveals Subgenome Divergence in the Regulation of Development and Stress Responses. The Plant Cell. DOI:10.1093/plcell/koab028 |
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