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Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat

Xie, Yilin; Ying, Songbei; Li, Zijuan; Zhang, Yu’e; Zhu, Jiafu; Zhang, Jinyu; Wang, Meiyue; Diao, Huishan; Wang, Haoyu; Zhang, Yuyun; Ye, Luhuan; Zhuang, Yili; Zhao, Fei; Teng, Wan; Zhang, Wenli; Tong, Yiping; Cho, Jungnam; Dong, Zhicheng; Xue, Yongbiao; Zhang, Yijing

Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat Thumbnail


Authors

Yilin Xie

Songbei Ying

Zijuan Li

Yu’e Zhang

Jiafu Zhu

Jinyu Zhang

Meiyue Wang

Huishan Diao

Haoyu Wang

Yuyun Zhang

Luhuan Ye

Yili Zhuang

Fei Zhao

Wan Teng

Wenli Zhang

Yiping Tong

Zhicheng Dong

Yongbiao Xue

Yijing Zhang



Abstract

Transposable elements (TEs) comprise ~85% of the common wheat genome, which are highly diverse among subgenomes, possibly contribute to polyploid plasticity, but the causality is only assumed. Here, by integrating data from gene expression cap analysis and epigenome profiling via hidden Markov model in common wheat, we detect a large proportion of enhancer-like elements (ELEs) derived from TEs producing nascent noncoding transcripts, namely ELE-RNAs, which are well indicative of the regulatory activity of ELEs. Quantifying ELE-RNA transcriptome across typical developmental stages reveals that TE-initiated ELE-RNAs are mainly from RLG_famc7.3 specifically expanded in subgenome A. Acquisition of spike-specific transcription factor binding likely confers spike-specific expression of RLG_famc7.3-initiated ELE-RNAs. Knockdown of RLG_famc7.3-initiated ELE-RNAs resulted in global downregulation of spike-specific genes and abnormal spike development. These findings link TE expansion to regulatory specificity and polyploid developmental plasticity, highlighting the functional impact of TE-driven regulatory innovation on polyploid evolution.

Citation

Xie, Y., Ying, S., Li, Z., Zhang, Y., Zhu, J., Zhang, J., …Zhang, Y. (2023). Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat. Nature Communications, 14(1), Article 7465. https://doi.org/10.1038/s41467-023-42771-9

Journal Article Type Article
Acceptance Date Oct 20, 2023
Online Publication Date Nov 17, 2023
Publication Date 2023
Deposit Date Nov 21, 2023
Publicly Available Date Nov 23, 2023
Journal Nature Communications
Publisher Nature Research
Peer Reviewed Peer Reviewed
Volume 14
Issue 1
Article Number 7465
DOI https://doi.org/10.1038/s41467-023-42771-9
Public URL https://durham-repository.worktribe.com/output/1945228

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Copyright Statement
This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.




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