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
aZhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China
bState Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
cWenzhou Medical University, Wenzhou 325027, China
dStructural Bioinformatics Laboratory, Biochemistry, ?bo Akademi University, Turku 20520, Finland
eDepartment of Otorhinolaryngology-Head and Neck Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200000, China
More InformationCorresponding 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.Keywords: FS-Hi-C,
Frozen sample,
Chromosome conformation
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