In Situ HiC

Timothy M Johanson; Rhys S Allan

doi:10.1007/978-1-0716-2140-0_18

In Situ HiC

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

Authors

Timothy M Johanson^{1

2}, Rhys S Allan^{3

4}

Affiliations

¹ The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia. johanson@wehi.edu.au.
² Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia. johanson@wehi.edu.au.
³ The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
⁴ Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.

PMID: 35103976
DOI: 10.1007/978-1-0716-2140-0_18

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.

MeSH terms

Cell Nucleus
Chromatin
DNA* / genetics
Genome*
Genomics

Substances

Chromatin
DNA