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BL-Hi-C以高灵敏度揭示了作物的三维基因组结构。

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

作者信息

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

机构信息

State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

出版信息

Hortic Res. 2024 Jan 16;11(3):uhae017. doi: 10.1093/hr/uhae017. eCollection 2024 Mar.

DOI:10.1093/hr/uhae017
PMID:38464474
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10923644/
Abstract

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 and . The Bouquet configuration of both and 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 gene loops in , , and . We observed that gene loops of exhibited conservation across , , and . While gene loops of syntenic exhibited conservation across and , variations in gene loops were evident among multiple paralogs 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.

摘要

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著背景噪声的阻碍，影响了它们检测精细三维基因组结构的能力。在本研究中，我们优化了桥连接头Hi-C技术（BL-Hi-C），以全面研究[具体植物1]和[具体植物2]的三维染色质景观。通过构建三维基因组模拟，阐明了[具体植物1]和[具体植物2]的花束构型。与传统Hi-C方法相比，优化后的BL-Hi-C背景噪声更低。利用这一优势，我们使用BL-Hi-C在[具体植物1]、[具体植物2]和[具体植物3]中鉴定基因环。我们观察到，[具体植物1]的基因环在[具体植物2]、[具体植物3]和[具体植物4]中表现出保守性。虽然同线[具体基因1]的基因环在[具体植物2]和[具体植物3]中表现出保守性，但同一物种内多个旁系同源基因[具体基因2]的基因环存在明显差异。总的来说，我们的研究结果突出了优化后的BL-Hi-C作为研究精细三维基因组组织的强大工具的高灵敏度。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eac1/10923644/779fded29a03/uhae017f5b.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eac1/10923644/1669301a6bf4/uhae017f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eac1/10923644/9d2107aec914/uhae017f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eac1/10923644/050fc16f6c4f/uhae017f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eac1/10923644/26e33279d819/uhae017f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eac1/10923644/fdd1abda4e62/uhae017f5a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eac1/10923644/779fded29a03/uhae017f5b.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eac1/10923644/1669301a6bf4/uhae017f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eac1/10923644/9d2107aec914/uhae017f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eac1/10923644/050fc16f6c4f/uhae017f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eac1/10923644/26e33279d819/uhae017f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eac1/10923644/fdd1abda4e62/uhae017f5a.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/eac1/10923644/779fded29a03/uhae017f5b.jpg

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Pan-3D genome analysis reveals structural and functional differentiation of soybean genomes.泛基因组分析揭示大豆基因组的结构和功能分化。
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