Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation.
IF: 17.694
Cited by: 64


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.


Gene Expression

MeSH terms

Gene Expression Regulation, Plant
Genome, Plant
Plant Proteins
Promoter Regions, Genetic
Transcription, Genetic


Zhao, Lun
Wang, Shuangqi
Cao, Zhilin
Ouyang, Weizhi
Zhang, Qing
Xie, Liang
Zheng, Ruiqin
Guo, Minrong
Ma, Meng
Hu, Zhe
Sung, Wing-Kin
Zhang, Qifa
Li, Guoliang
Li, Xingwang

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