Integrative analysis of reference epigenomes in 20 rice varieties

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, Qinghua Zhang, Qifa Zhang, Guoliang Li () and Xingwang Li ()
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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
Qinghua Zhang: Huazhong Agricultural University
Qifa Zhang: Huazhong Agricultural University
Guoliang Li: Huazhong Agricultural University
Xingwang Li: Huazhong Agricultural University

Nature Communications, 2020, vol. 11, issue 1, 1-16

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-16457-5

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