title: Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell.
abstract: Hi-C is a powerful method that provides pairwise information on genomic regions in spatial proximity in the nucleus. Hi-C requires millions of cells as input and, as genome organization varies from cell to cell, a limitation of Hi-C is that it only provides a population average of genome conformations. We developed single-cell Hi-C to create snapshots of thousands of chromatin interactions that occur simultaneously in a single cell. To adapt Hi-C to single-cell analysis, we modified the protocol to include in-nucleus ligation. This enables the isolation of single nuclei carrying Hi-C-ligated DNA into separate tubes, followed by reversal of cross-links, capture of biotinylated ligation junctions on streptavidin-coated magnetic beads and PCR amplification of single-cell Hi-C libraries. The entire laboratory protocol can be carried out in 1 week, and although we have demonstrated its use in mouse T helper (TH1) cells, it should be applicable to any cell type or species for which standard Hi-C has been successful. We also developed an analysis pipeline to filter noise and assess the quality of data sets in a few hours. Although the interactome maps produced by single-cell Hi-C are sparse, the data provide useful information to understand cellular variability in nuclear genome organization and chromosome structure. Standard wet and dry laboratory skills in molecular biology and computational analysis are required.
authors.affiliation: Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK.
authors.forename: Takashi
authors.initials: T
authors.lastname: Nagano
authors.affiliation: Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel.
authors.forename: Yaniv
authors.identifier: http://orcid.org/0000-0003-3461-9621
authors.initials: Y
authors.lastname: Lubling
authors.affiliation: Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel.
authors.forename: Eitan
authors.identifier: http://orcid.org/0000-0002-2896-3349
authors.initials: E
authors.lastname: Yaffe
authors.affiliation: Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK.
authors.forename: Steven W
authors.initials: SW
authors.lastname: Wingett
authors.affiliation: Epigenetics Programme, The Babraham Institute, Cambridge, UK.
authors.forename: Wendy
authors.initials: W
authors.lastname: Dean
authors.affiliation: Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel.
authors.forename: Amos
authors.initials: A
authors.lastname: Tanay
authors.affiliation: Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK.
authors.forename: Peter
authors.initials: P
authors.lastname: Fraser
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D002843:Chromatin / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D016678:Genome; D023281:Genomics / Q000379:methods; D051379:Mice; D059010:Single-Cell Analysis / Q000379:methods*; D018417:Th1 Cells / Q000378:metabolism
chemical_list: D002843:Chromatin