Chromatin interaction maps reveal genetic regulation for quantitative traits in maize

Yong Peng, Dan Xiong, Lun Zhao, Weizhi Ouyang, Shuangqi Wang, Jun Sun, Qing Zhang, Pengpeng Guan, Liang Xie, Wenqiang Li, Guoliang Li (), Jianbing Yan () and Xingwang Li ()
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Yong Peng: Huazhong Agricultural University
Dan Xiong: Huazhong Agricultural University
Lun Zhao: Huazhong Agricultural University
Weizhi Ouyang: Huazhong Agricultural University
Shuangqi Wang: Huazhong Agricultural University
Jun Sun: Huazhong Agricultural University
Qing Zhang: Huazhong Agricultural University
Pengpeng Guan: Huazhong Agricultural University
Liang Xie: Huazhong Agricultural University
Wenqiang Li: Huazhong Agricultural University
Guoliang Li: Huazhong Agricultural University
Jianbing Yan: Huazhong Agricultural University
Xingwang Li: Huazhong Agricultural University

Nature Communications, 2019, vol. 10, issue 1, 1-11

Abstract: Abstract Chromatin loops connect regulatory elements to their target genes. They serve as bridges between transcriptional regulation and phenotypic variation in mammals. However, spatial organization of regulatory elements and its impact on gene expression in plants remain unclear. Here, we characterize epigenetic features of active promoter proximal regions and candidate distal regulatory elements to construct high-resolution chromatin interaction maps for maize via long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). The maps indicate that chromatin loops are formed between regulatory elements, and that gene pairs between promoter proximal regions tend to be co-expressed. The maps also demonstrated the topological basis of quantitative trait loci which influence gene expression and phenotype. Many promoter proximal regions are involved in chromatin loops with distal regulatory elements, which regulate important agronomic traits. Collectively, these maps provide a high-resolution view of 3D maize genome architecture, and its role in gene expression and phenotypic variation.

Date: 2019
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DOI: 10.1038/s41467-019-10602-5

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