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
- 1National 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;
- 2University of the Chinese Academy of Sciences, Beijing, 100049, China;
- 3The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China;
- 4State Key Laboratory for Crop Genetics and Germplasm Enhancement, Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry (CIC-MCP), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China;
- 5Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China;
- 6Henan University, School of Life Science, Kaifeng, Henan 457000, China;
- 7Beijing Institute of Genomics, Chinese Academy of Sciences, and National Centre for Bioinformation, Beijing 100101 China;
- 8Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China;
- 9State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
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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.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
