Genome Research
Abstract
More than 80% of the wheat genome consists of transposable elements (TEs), which act as one major driver 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 inTriticum urartu, together with epigenomic profiles. Most TF-binding sites (TFBS) 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 TFBS share significantly high sequence similarity with TE-embedded TFBS. These non-TE TFBS 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.
| 论文编号: | DOI:10.1101/gr.275658.121 |
| 论文题目: | Evolutionary Rewiring of the Wheat Transcriptional Regulatory Network by Lineage-Specific Transposable Elements |
| 英文论文题目: | Evolutionary Rewiring of the Wheat Transcriptional Regulatory Network by Lineage-Specific Transposable Elements |
| 第一作者: | Yuyun Zhang, Zijuan Li, Yu'e Zhang, Kande Lin, Yuan Peng, Luhuan Ye, Yili Zhuang, Meiyue Wang, Yilin Xie, Jingyu Guo, Wan Teng, Yiping Tong, Wenli Zhang, Yongbiao Xue, Zhaobo Lang and Yijing Zhang |
| 英文第一作者: | Yuyun Zhang, Zijuan Li, Yu'e Zhang, Kande Lin, Yuan Peng, Luhuan Ye, Yili Zhuang, Meiyue Wang, Yilin Xie, Jingyu Guo, Wan Teng, Yiping Tong, Wenli Zhang, Yongbiao Xue, Zhaobo Lang and Yijing Zhang |
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| 发表年度: | 2021-09-15 |
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| 摘要: | More than 80% of the wheat genome consists of transposable elements (TEs), which act as one major driver 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 inTriticum urartu, together with epigenomic profiles. Most TF-binding sites (TFBS) 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 TFBS share significantly high sequence similarity with TE-embedded TFBS. These non-TE TFBS 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. |
| 英文摘要: | More than 80% of the wheat genome consists of transposable elements (TEs), which act as one major driver 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 inTriticum urartu, together with epigenomic profiles. Most TF-binding sites (TFBS) 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 TFBS share significantly high sequence similarity with TE-embedded TFBS. These non-TE TFBS 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. |
| 刊物名称: | Genome Research |
| 英文刊物名称: | Genome Research |
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| 其它备注: | Yuyun Zhang, Zijuan Li, Yu e Zhang, Kande Lin, Yuan Peng, Luhuan Ye, Yili Zhuang, Meiyue Wang, Yilin Xie, Jingyu Guo, Wan Teng, Yiping Tong, Wenli Zhang, Yongbiao Xue, Zhaobo Lang and Yijing Zhang. Evolutionary Rewiring of the Wheat Transcriptional Regulatory Network by Lineage-Specific Transposable Elements. Genome Research. DOI:10.1101/gr.275658.121 |
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