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

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

doi:10.1016/j.jgg.2020.11.002

Volume 48 Issue 3

Mar. 2021

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Article Navigation > Journal of Genetics and Genomics > 2021 > 48(3): 237-247

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

doi: 10.1016/j.jgg.2020.11.002

Wu Zheng^{a, b, c, #},
Zhaoen Yang^{a, b, #},
Xiaoyang Ge^{a, b, #},
Yijia Feng^c,
Ye Wang^b,
Chengwei Liu^c,
Yanan Luan^c,
Kun Cai^a,
Serhii Vakal^d,
Feng You^c,
Wei Guo^c,
Wei Wang^e,
Zhenhua Feng^a,
Fuguang Li^{a, b}

a
Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China
b
State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
c
Wenzhou Medical University, Wenzhou 325027, China
d
Structural Bioinformatics Laboratory, Biochemistry, Åbo Akademi University, Turku 20520, Finland
e
Department of Otorhinolaryngology-Head and Neck Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200000, China

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Corresponding author: E-mail address: aylifug@caas.cn (Fuguang Li)
Received Date: 2020-10-15
Accepted Date: 2020-11-19
Rev Recd Date: 2020-11-17

Available Online: 2020-12-01

Publish Date: 2021-03-20

Abstract

Abstract

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-Hi-C outperforms the in situ Hi-C in terms of library quality, reproducibility, and valid interactions. Thus, FS-Hi-C 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.
- FS-Hi-C,
- Frozen sample,
- Chromosome conformation

These authors contributed equally to this work.

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References(35)

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