Chromosome Conformation Capture Followed by Genome-Wide Sequencing (Hi-C) in 
Drosophila Embryos

Cardamone, Francesco; Zhan, Yinxiu; Iovino, Nicola; Zenk, Fides

doi:10.1007/978-1-0716-3143-0_4

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Chromosome Conformation Capture Followed by Genome-Wide Sequencing (Hi-C) in Drosophila Embryos

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Cardamone, Francesco
Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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Iovino, Nicola
Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society;

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https://link.springer.com/protocol/10.1007/978-1-0716-3143-0_4
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Citation

Cardamone, F., Zhan, Y., Iovino, N., & Zenk, F. (2023). Chromosome Conformation Capture Followed by Genome-Wide Sequencing (Hi-C) in Drosophila Embryos. Methods in Molecular Biology, 2655, 41-55. doi:10.1007/978-1-0716-3143-0_4.

Cite as: https://hdl.handle.net/21.11116/0000-000D-4548-5

Abstract

This protocol provides specific details on how to perform Hi-C, the genome-wide version of Chromosome Conformation Capture (3C) followed by high-throughput sequencing, in Drosophila embryos. Hi-C provides a genome-wide population-averaged snapshot of the 3D genome organization within nuclei. In Hi-C, formaldehyde-cross-linked chromatin is enzymatically digested using restriction enzymes; digested fragments are biotinylated and subjected to proximity ligation; ligated fragments are purified using streptavidin followed by paired-end sequencing. Hi-C allows the detection of higher order folding structures such as topologically associated domains (TADs) and active/inactive compartments (A/B compartments, respectively). Performing this assay in developing embryos gives the unique opportunity to investigate dynamic chromatin changes when 3D chromatin structure is established in embryogenesis.