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. 2022:2458:333-343.
doi: 10.1007/978-1-0716-2140-0_18.

In Situ HiC

Timothy M Johanson  1   2 , Rhys S Allan  3   4
Affiliations

In Situ HiC

Timothy M Johanson et al. Methods Mol Biol. 2022.

Abstract

In situ HiC uses the relative frequency of DNA-DNA ligation events to reconstruct the three-dimensional architecture of a genome. As such, restriction enzyme digested ends of genomic DNA within fixed nuclei are tagged with biotinylated dNTPs. DNA-DNA ligation events generated via proximity ligation are then captured, amplified and next generation sequenced to determine their linear genomic position, but also their three-dimensional relationship. Here, we describe these steps in detail.

Keywords: Chromatin architecture; Chromosome conformation capture; Genome organization; In situ HiC.

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References

    1. Furlan-Magaril M, Varnai C, Nagano T, Fraser P (2015) 3D genome architecture from populations to single cells. Curr Opin Genet Dev 31:36–41. https://doi.org/10.1016/j.gde.2015.04.004 - DOI - PubMed
    1. Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295(5558):1306–1311. https://doi.org/10.1126/science.1067799 - DOI - PubMed
    1. Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38(11):1348–1354. https://doi.org/10.1038/ng1896 - DOI - PubMed
    1. Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C, Green RD, Dekker J (2006) Chromosome conformation capture carbon copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 16(10):1299–1309. https://doi.org/10.1101/gr.5571506 - DOI - PubMed - PMC
    1. Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES, Aiden EL (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159(7):1665–1680. https://doi.org/10.1016/j.cell.2014.11.021 - DOI - PubMed - PMC

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