Zhang Yuyun, Li Zijuan, Zhang Yu'e, Lin Kande, Peng Yuan, Ye Luhuan, Zhuang Yili, Wang Meiyue, Xie Yilin, Guo Jingyu, Teng Wan, Tong Yiping, Zhang Wenli, Xue Yongbiao, Lang Zhaobo, Zhang Yijing
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
University of the Chinese Academy of Sciences, Beijing, 100049, China.
Genome Res. 2021 Dec;31(12):2276-2289. doi: 10.1101/gr.275658.121. Epub 2021 Sep 9.
More than 80% of the wheat genome consists of transposable elements (TEs), which act as major drivers of wheat genome evolution. However, their contributions to the regulatory evolution of wheat adaptations remain largely unclear. Here, we created genome-binding maps for 53 transcription factors (TFs) underlying environmental responses by leveraging DAP-seq in , together with epigenomic profiles. Most TF binding sites (TFBSs) located distally from genes are embedded in TEs, whose functional relevance is supported by purifying selection and active epigenomic features. About 24% of the non-TE TFBSs share significantly high sequence similarity with TE-embedded TFBSs. These non-TE TFBSs have almost no homologous sequences in non-Triticeae species and are potentially derived from Triticeae-specific TEs. The expansion of TE-derived TFBS linked to wheat-specific gene responses, suggesting TEs are an important driving force for regulatory innovations. Altogether, TEs have been significantly and continuously shaping regulatory networks related to wheat genome evolution and adaptation.
超过80%的小麦基因组由转座元件（TEs）组成，这些转座元件是小麦基因组进化的主要驱动力。然而，它们对小麦适应性调控进化的贡献在很大程度上仍不清楚。在这里，我们通过利用DAP-seq技术，结合表观基因组图谱，为53个参与环境响应的转录因子（TFs）创建了基因组结合图谱。大多数位于基因远端的转录因子结合位点（TFBSs）嵌入在转座元件中，纯化选择和活跃的表观基因组特征支持了它们的功能相关性。约24%的非转座元件TFBSs与嵌入转座元件的TFBSs具有显著的高序列相似性。这些非转座元件TFBSs在非小麦族物种中几乎没有同源序列，可能源自小麦族特有的转座元件。与小麦特异性基因响应相关的转座元件衍生TFBSs的扩增，表明转座元件是调控创新的重要驱动力。总之，转座元件一直在显著且持续地塑造与小麦基因组进化和适应性相关的调控网络。
