TY - JOUR
T1 - Freeze substitution Hi-C, a convenient and cost-effective method for capturing the natural 3D chromatin conformation from frozen samples
AU - Zheng, W.
AU - Yang, Z.
AU - Ge, X.
AU - Feng, Y.
AU - Wang, Y.
AU - Liu, C.
AU - Luan, Y.
AU - Cai, K.
AU - Vakal, S.
AU - You, F.
AU - Guo, W.
AU - Wang, W.
AU - Feng, Z.
AU - Li, F.
PY - 2021
Y1 - 2021
N2 - Chromatin interactions functionally affect genome architecture and gene regulation, but to date, only fresh samples must be used in 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 developed 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 heatmaps and delineating A/B compartments and TADs, 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.
AB - Chromatin interactions functionally affect genome architecture and gene regulation, but to date, only fresh samples must be used in 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 developed 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 heatmaps and delineating A/B compartments and TADs, 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.
KW - FS-Hi-C
KW - Gossypium hirsutum
KW - Drosophila melanogaster
KW - chromosome conformation
KW - frozen sample
UR - http://www.scopus.com/inward/record.url?eid=2-s2.0-85100608968&partnerID=MN8TOARS
U2 - 10.1016/j.jgg.2020.11.002
DO - 10.1016/j.jgg.2020.11.002
M3 - Article
SN - 1673-8527
VL - 48
SP - 237
EP - 247
JO - Journal of Genetics and Genomics
JF - Journal of Genetics and Genomics
IS - 3
ER -