An atlas of wheat epigenetic regulatory elements reveals subgenome-divergence in the regulation of development and stress responses
An atlas of wheat epigenetic regulatory elements reveals subgenome-divergence in the regulation of development and stress responses
复制标题
小麦表观遗传调控元件图谱揭示了发育和胁迫反应调控中的亚基因组差异
DOI：
10.1093/plcell/koab028
复制
发表时间：
2021
期刊：
影响因子：
--
通讯作者：
Yijing Zhang
中科院分区：
文献类型：
--
作者：
Meiyue Wang;Zijuan Li;Yu’e Zhang;Yuyun Zhang;Yilin Xie;Luhuan Ye;Yili Zhuang;K;e Lin;Fei Zhao;Jingyu Guo;Wan Teng;Wenli Zhang;Yiping Tong;Yongbiao Xue;Yijing Zhang
小麦（Triticum aestivum）具有大的异源六倍体基因组。亚基因组趋异调控有助于基因组可塑性和多倍体小麦的驯化。然而，在小麦基因组中编码的特异性决定亚基因组趋异的时空调控在很大程度上尚未探索。基因组的巨大规模和复杂性是剖析调控特异性的主要障碍。在这里，我们比较了表观基因组和转录组在不同的发育和环境条件下，从一个大的样本集。成千上万的远端表观遗传调控元件（远端epiREs）与其靶启动子特异性连接，具有协调的表观基因组变化。我们揭示了同源调控元件的亚基因组趋异活性受到特定表观遗传特征的影响。组织特异性的亚基因组趋异epiRE调节与Polycomb复合物和脱甲基酶介导的H3K27me3的动态调节相关。此外，定量表观基因组学方法检测到关键的应激反应顺式和反式作用因子，通过DNA亲和纯化和测序验证，并证明了epiRE序列背景，表观遗传因子和转录因子之间的协调相互作用，调节亚基因组趋异的转录响应外部变化。总之，这项研究为阐明六倍体小麦中的epiRE调节组学和亚基因组趋异调节提供了丰富的资源，并为解释遗传和表观遗传相互作用在调节多倍体小麦的益处方面提供了新的线索。
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.