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

Author

Listed:
  • Yilin Xie

    (Fudan University
    Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    University of the Chinese Academy of Sciences)

  • Songbei Ying

    (Fudan University)

  • Zijuan Li

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    University of the Chinese Academy of Sciences)

  • Yu’e Zhang

    (University of the Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Jiafu Zhu

    (Guangzhou University)

  • Jinyu Zhang

    (Fudan University
    Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    University of the Chinese Academy of Sciences)

  • Meiyue Wang

    (Fudan University)

  • Huishan Diao

    (Fudan University)

  • Haoyu Wang

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    Henan University, School of Life Science)

  • Yuyun Zhang

    (Fudan University
    Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    University of the Chinese Academy of Sciences)

  • Luhuan Ye

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    University of the Chinese Academy of Sciences)

  • Yili Zhuang

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    University of the Chinese Academy of Sciences)

  • Fei Zhao

    (Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
    University of the Chinese Academy of Sciences)

  • Wan Teng

    (University of the Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Wenli Zhang

    (Nanjing Agricultural University)

  • Yiping Tong

    (University of the Chinese Academy of Sciences
    Chinese Academy of Sciences)

  • Jungnam Cho

    (Durham University)

  • Zhicheng Dong

    (Guangzhou University)

  • Yongbiao Xue

    (University of the Chinese Academy of Sciences
    Chinese Academy of Sciences
    Chinese Academy of Sciences, and China National Centre for Bioinformation
    Yangzhou University)

  • Yijing Zhang

    (Fudan University)

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.

Suggested Citation

  • 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 & Yipi, 2023. "Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42771-9
    DOI: 10.1038/s41467-023-42771-9
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    as
    1. Yuyun Zhang & Zijuan Li & Jinyi Liu & Yu’e Zhang & Luhuan Ye & Yuan Peng & Haoyu Wang & Huishan Diao & Yu Ma & Meiyue Wang & Yilin Xie & Tengfei Tang & Yili Zhuang & Wan Teng & Yiping Tong & Wenli Zha, 2022. "Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
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