Freeze substitution Hi-C, a convenient and cost-effective method for capturing the natural 3D chromatin conformation from frozen samples

文献类型： 外文期刊

第一作者： Zheng, Wu

作者： Zheng, Wu;Yang, Zhaoen;Ge, Xiaoyang;Cai, Kun;Feng, Zhenhua;Li, Fuguang;Wang, Ye;Feng, Yijia;Liu, Chengwei;Luan, Yanan;You, Feng;Guo, Wei;Vakal, Serhii;Wang, Wei

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关键词： FS-Hi-C; Frozen sample; Chromosome conformation; Drosophila melanogaster; Gossypium hirsutum

期刊名称：JOURNAL OF GENETICS AND GENOMICS （ 影响因子：4.275； 五年影响因子：5.223 ）

ISSN： 1673-8527

年卷期： 2021 年 48 卷 3 期

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收录情况： SCI

摘要： Chromatin interactions functionally affect genome architecture and gene regulation, but to date, only fresh samples must be used in High-through chromosome conformation capture (Hi-C) to keep natural chromatin conformation intact. This requirement has impeded the advancement of 3D genome research by limiting sample collection and storage options for researchers and severely limiting the number of samples that can be processed in a short time. Here, we develop a freeze substitution Hi-C (FS-Hi-C) technique that overcomes the need for fresh samples. FS-Hi-C can be used with samples stored in liquid nitrogen (LN2): the water in a vitreous form in the sample cells is replaced with ethanol via automated freeze substitution. After confirming that the FS step preserves the natural chromosome conformation during sample thawing, we tested the performance of FS-Hi-C with Drosophila melanogaster and Gossypium hirsutum. Beyond allowing the use of frozen samples and confirming that FS-Hi-C delivers robust data for generating contact heat maps and delineating A/B compartments and topologically associating domains, we found that FS-HiC outperforms the in situ Hi-C in terms of library quality, reproducibility, and valid interactions. Thus, FS-HiC will probably extend the application of 3D genome structure analysis to the vast number of experimental contexts in biological and medical research for which Hi-C methods have been unfeasible to date. Copyright (C) 2020, The Authors. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Limited and Science Press.

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