数字农科院2.0

BL-Hi-C reveals the 3D genome structure of Brassica crops with high sensitivity

文献类型： 外文期刊

作者： Lupeng Zhang;Ranze Zhao;Jianli Liang;Xu Cai;Lei Zhang;Huiling Guo;Zhicheng Zhang;Jian Wu;Xiaowu Wang

作者机构：

期刊名称： Horticulture Research

ISSN： 2662-6810

年卷期： 2024 年 11 卷 3 期

页码：

收录情况： SCIE（2024版） ; ; CSCD（2023-2024年度） ; ; 科技核心（2024版） ; ; 农林核心（2020版）

摘要： High-throughput Chromatin Conformation Capture (Hi-C) technologies can be used to investigate the three-dimensional genomic structure of plants. However, the practical utility of these technologies is impeded by significant background noise, hindering their capability in detecting fine 3D genomic structures. In this study, we optimized the Bridge Linker Hi-C technology (BL-Hi-C) to comprehensively investigate the 3D chromatin landscape of Brassica rapa and Brassica oleracea. The Bouquet configuration of both B. rapa and B. oleracea was elucidated through the construction of a 3D genome simulation. The optimized BL-Hi-C exhibited lower background noise compared to conventional Hi-C methods. Taking this advantage, we used BL-Hi-C to identify FLC gene loops in Arabidopsis, B. rapa, and B. oleracea. We observed that gene loops of FLC2 exhibited conservation across Arabidopsis, B. rapa, and B. oleracea. While gene loops of syntenic FLCs exhibited conservation across B. rapa and B. oleracea, variations in gene loops were evident among multiple paralogs FLCs within the same species. Collectively, our findings highlight the high sensitivity of optimized BL-Hi-C as a powerful tool for investigating the fine 3D genomic organization.

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