Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation

Lun Zhao, Shuangqi Wang, Zhilin Cao, Weizhi Ouyang, Qing Zhang, Liang Xie, Ruiqin Zheng, Minrong Guo, Meng Ma, Zhe Hu, Wing-Kin Sung, Qifa Zhang, Guoliang Li () and Xingwang Li ()
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Lun Zhao: Huazhong Agricultural University
Shuangqi Wang: Huazhong Agricultural University
Zhilin Cao: Huazhong Agricultural University
Weizhi Ouyang: Huazhong Agricultural University
Qing Zhang: Huazhong Agricultural University
Liang Xie: Huazhong Agricultural University
Ruiqin Zheng: Huazhong Agricultural University
Minrong Guo: Huazhong Agricultural University
Meng Ma: Huazhong Agricultural University
Zhe Hu: Huazhong Agricultural University
Wing-Kin Sung: National University of Singapore
Qifa Zhang: Huazhong Agricultural University
Guoliang Li: Huazhong Agricultural University
Xingwang Li: Huazhong Agricultural University

Nature Communications, 2019, vol. 10, issue 1, 1-13

Abstract: Abstract Insight into high-resolution three-dimensional genome organization and its effect on transcription remains largely elusive in plants. Here, using a long-read ChIA-PET approach, we map H3K4me3- and RNA polymerase II (RNAPII)-associated promoter–promoter interactions and H3K9me2-marked heterochromatin interactions at nucleotide/gene resolution in rice. The chromatin architecture is separated into different independent spatial interacting modules with distinct transcriptional potential and covers approximately 82% of the genome. Compared to inactive modules, active modules possess the majority of active loop genes with higher density and contribute to most of the transcriptional activity in rice. In addition, promoter–promoter interacting genes tend to be transcribed cooperatively. In contrast, the heterochromatin-mediated loops form relative stable structure domains in chromatin configuration. Furthermore, we examine the impact of genetic variation on chromatin interactions and transcription and identify a spatial correlation between the genetic regulation of eQTLs and e-traits. Thus, our results reveal hierarchical and modular 3D genome architecture for transcriptional regulation in rice.

Date: 2019
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DOI: 10.1038/s41467-019-11535-9

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