조정남 (Durham University)

한빛사 논문

조회747

Durham University

Nat. Commun., Nov 17 2023, 14 (1) | https://doi.org/10.1038/s41467-023-42771-9 Transposable element-initiated enhancer-like elements generate the subgenome-biased spike specificity of polyploid wheat

Yilin Xie^1,2,3,11, Songbei Ying^1,11, Zijuan Li^2,3,11, Yu’e Zhang^3,4,11, Jiafu Zhu^5,11, Jinyu Zhang^1,2,3, Meiyue Wang¹, Huishan Diao¹, Haoyu Wang^2,6, uyun Zhang^1,2,3, Luhuan Ye^2,3, Yili Zhuang^2,3, Fei Zhao^2,3, Wan Teng^3,4, Wenli Zhang⁷, Yiping Tong^3,4, Jungnam Cho⁸, Zhicheng Dong⁵ , Yongbiao Xue^3,4,9,10 & Yijing Zhang¹

¹State 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.

²National 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, 300 Fenglin Road, Shanghai 200032, China.

³University of the Chinese Academy of Sciences, Beijing 100049, China.

⁴State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, and The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.

⁵Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.

⁶Henan University, School of Life Science, Kaifeng, Henan 457000, China.

⁷State Key Laboratory for Crop Genetics and Germplasm Enhancement, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing, Jiangsu 210095, China.

⁸Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom.

⁹Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Centre for Bioinformation, Beijing 100101, China.

¹⁰Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.

¹¹These authors contributed equally: Yilin Xie, Songbei Ying, Zijuan Li, Yu’e Zhang, Jiafu Zhu.

Corresponding authors : Correspondence to Jungnam Cho, Zhicheng Dong, Yongbiao Xue or 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.

논문정보

형식Research article
게재일2023년 11월 (BRIC 등록일 2023-11-18)
연구진국외 연구진
분야 생명과학 > 유전자발현

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