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

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.

• 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, Jungnam Cho, Zhicheng Dong, Yongbiao Xue, Yijing Zhang
• Journal: Nature communications (Nat Commun) Vol. 14 Issue 1 Pg. 7465 (11 17 2023) ISSN: 2041-1723 [Electronic] England
• PMID: 37978184 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © 2023. The Author(s).

Chemical References

• DNA Transposable Elements
• RNA

Topics

• DNA Transposable Elements (genetics)
• Triticum (genetics)
• Gene Expression Regulation
• Polyploidy
• Transcriptome
• RNA