IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-42771-9.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-42771-9
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-42771-9?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Rongrong Zhang & Yu Wu & Xiangru Qu & Wenjuan Yang & Qin Wu & Lin Huang & Qiantao Jiang & Jian Ma & Yazhou Zhang & Pengfei Qi & Guoyue Chen & Yunfeng Jiang & Youliang Zheng & Xiaojie Wang & Yuming Wei, 2024. "The RING-finger ubiquitin E3 ligase TaPIR1 targets TaHRP1 for degradation to suppress chloroplast function," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Chao Fang & Ning Jiang & Scott J. Teresi & Adrian E. Platts & Gaurav Agarwal & Chad Niederhuth & Patrick P. Edger & Jiming Jiang, 2024. "Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    3. Zijuan Li & Yuyun Zhang & Ci-Hang Ding & Yan Chen & Haoyu Wang & Jinyu Zhang & Songbei Ying & Meiyue Wang & Rongzhi Zhang & Jinyi Liu & Yilin Xie & Tengfei Tang & Huishan Diao & Luhuan Ye & Yili Zhuan, 2023. "LHP1-mediated epigenetic buffering of subgenome diversity and defense responses confers genome plasticity and adaptability in allopolyploid wheat," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-42771-9. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.