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.

中文翻译：

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BL-hi-C 高灵敏度揭示芸苔属作物的 3D 基因组结构

高通量染色质构象捕获（Hi-C）技术可用于研究植物的三维基因组结构。然而，这些技术的实际应用受到显着背景噪声的阻碍，从而阻碍了它们检测精细 3D 基因组结构的能力。在本研究中，我们优化了 Bridge Linker Hi-C 技术 (BL-Hi-C)，以全面研究白菜和甘蓝的 3D 染色质景观。通过构建 3D 基因组模拟，阐明了白菜和甘蓝的花束结构。与传统的 Hi-C 方法相比，优化的 BL-Hi-C 表现出更低的背景噪声。利用这一优势，我们使用 BL-Hi-C 来鉴定拟南芥、白菜和甘蓝中的 FLC 基因环。我们观察到 FLC2 的基因环在拟南芥、白菜和甘蓝中表现出保守性。虽然同线 FLC 的基因环在白菜和甘蓝中表现出保守性，但同一物种内的多个旁系同源 FLC 中基因环的变化很明显。总的来说，我们的研究结果强调了优化的 BL-Hi-C 作为研究精细 3D 基因组组织的强大工具的高灵敏度。