Chromatin interaction maps reveal genetic regulation for quantitative traits in maize
Chromatin interaction maps reveal genetic regulation for quantitative traits in maize
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染色质相互作用图揭示了玉米数量性状的遗传调控
DOI：
10.1038/s41467-019-10602-5
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发表时间：
2019-06-14
影响因子：
16.6
通讯作者：
Li, Xingwang
中科院分区：
文献类型：
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作者：
Peng, Yong;Xiong, Dan;Li, Xingwang
染色质环将调控元件连接到它们的靶基因。它们在哺乳动物中充当转录调控和表型变异之间的桥梁。然而，调控元件的空间组织及其对植物基因表达的影响仍不清楚。在这里，我们表征活性启动子近端区域和候选远端调控元件的表观遗传特征，通过双端标签测序（ChIA-PET）的长读染色质相互作用分析构建玉米的高分辨率染色质相互作用图谱。这些图谱表明，染色质环之间形成的调控元件，和基因对之间的启动子近端区域往往是共表达。这些图谱还揭示了影响基因表达和表型的数量性状基因座的拓扑基础。许多启动子近端区域参与了具有远端调控元件的染色质环，调控重要的农艺性状。总的来说，这些图谱提供了3D玉米基因组结构及其在基因表达和表型变异中的作用的高分辨率视图。
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.