NATURE COMMUNICATIONS|         (2019) 10:3640 | https://doi.org/10.1038/s41467-019-11535-9 | www.nature.com/naturecommunications11234567890

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, Xingwang Li

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

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