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Integrative analysis of reference epigenomes in 20 rice varieties

Author

Listed:
  • Lun Zhao

    (Huazhong Agricultural University)

  • Liang Xie

    (Huazhong Agricultural University)

  • Qing Zhang

    (Huazhong Agricultural University)

  • Weizhi Ouyang

    (Huazhong Agricultural University)

  • Li Deng

    (Huazhong Agricultural University)

  • Pengpeng Guan

    (Huazhong Agricultural University)

  • Meng Ma

    (Huazhong Agricultural University)

  • Yue Li

    (Huazhong Agricultural University)

  • Ying Zhang

    (Huazhong Agricultural University)

  • Qin Xiao

    (Huazhong Agricultural University)

  • Jingwen Zhang

    (Huazhong Agricultural University)

  • Hongmeijuan Li

    (Huazhong Agricultural University)

  • Shunyao Wang

    (Huazhong Agricultural University)

  • Jiangwei Man

    (Huazhong Agricultural University)

  • Zhilin Cao

    (Huazhong Agricultural University
    Henan University of Engineering)

  • Qinghua Zhang

    (Huazhong Agricultural University)

  • Qifa Zhang

    (Huazhong Agricultural University)

  • Guoliang Li

    (Huazhong Agricultural University
    Huazhong Agricultural University)

  • Xingwang Li

    (Huazhong Agricultural University)

Abstract

Epigenomic modifications are instrumental for transcriptional regulation, but comprehensive reference epigenomes remain unexplored in rice. Here, we develop an enhanced chromatin immunoprecipitation (eChIP) approach for plants, and generate genome-wide profiling of five histone modifications and RNA polymerase II occupancy with it. By integrating chromatin accessibility, DNA methylation, and transcriptome datasets, we construct comprehensive epigenome landscapes across various tissues in 20 representative rice varieties. Approximately 81.8% of rice genomes are annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provides insight into transcriptional regulation. We identify extensive enhancer-like promoters with potential enhancer function on transcriptional regulation through chromatin interactions. Active and repressive histone modifications and the predicted enhancers vary largely across tissues, whereas inactive chromatin states are relatively stable. Together, these datasets constitute a valuable resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation.

Suggested Citation

  • Lun Zhao & Liang Xie & Qing Zhang & Weizhi Ouyang & Li Deng & Pengpeng Guan & Meng Ma & Yue Li & Ying Zhang & Qin Xiao & Jingwen Zhang & Hongmeijuan Li & Shunyao Wang & Jiangwei Man & Zhilin Cao & Qin, 2020. "Integrative analysis of reference epigenomes in 20 rice varieties," Nature Communications, Nature, vol. 11(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16457-5
    DOI: 10.1038/s41467-020-16457-5
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    Cited by:

    1. 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.
    2. Xi Wang & Juan Li & Linqian Han & Chengyong Liang & Jiaxin Li & Xiaoyang Shang & Xinxin Miao & Zi Luo & Wanchao Zhu & Zhao Li & Tianhuan Li & Yongwen Qi & Huihui Li & Xiaoduo Lu & Lin Li, 2023. "QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    3. Jinfei Zhang & Yuyi Zhang & Jingguang Chen & Mengfan Xu & Xinyu Guan & Cui Wu & Shunan Zhang & Hongye Qu & Jinfang Chu & Yifeng Xu & Mian Gu & Ying Liu & Guohua Xu, 2024. "Sugar transporter modulates nitrogen-determined tillering and yield formation in rice," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    4. Yong Zhou & Zhichao Yu & Dmytro Chebotarov & Kapeel Chougule & Zhenyuan Lu & Luis F. Rivera & Nagarajan Kathiresan & Noor Al-Bader & Nahed Mohammed & Aseel Alsantely & Saule Mussurova & João Santos & , 2023. "Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    5. Chao He & Siteng Bi & Yuqi Li & Chengxiang Song & Heping Zhang & Xintong Xu & Qiang Li & Sulaiman Saeed & Wei Chen & Chunjie Zhao & Caixia Lan & Handong Su & Hailiang Mao & Wenhao Yan, 2024. "Dynamic atlas of histone modifications and gene regulatory networks in endosperm of bread wheat," Nature Communications, Nature, vol. 15(1), pages 1-16, December.

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