Evolutionary rewiring of the wheat transcriptional regulatory network by lineage-specific transposable elements
- Yuyun Zhang1,2,10,
- Zijuan Li1,2,10,
- Yu'e Zhang2,3,10,
- Kande Lin4,10,
- Yuan Peng1,2,5,
- Luhuan Ye1,2,
- Yili Zhuang1,2,
- Meiyue Wang1,2,
- Yilin Xie1,2,
- Jingyu Guo1,6,
- Wan Teng2,3,
- Yiping Tong2,3,
- Wenli Zhang4,
- Yongbiao Xue2,3,7,8,
- Zhaobo Lang1,2,5 and
- Yijing Zhang1,2,9
+ Author Affiliations
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↵10 These authors contributed equally to this work.
Abstract
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 Triticum urartu, 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.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.275658.121.
- Received April 15, 2021.
- Accepted September 1, 2021.
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