title: Exploiting native forces to capture chromosome conformation in mammalian cell nuclei.
abstract: Mammalian interphase chromosomes fold into a multitude of loops to fit the confines of cell nuclei, and looping is tightly linked to regulated function. Chromosome conformation capture (3C) technology has significantly advanced our understanding of this structure-to-function relationship. However, all 3C-based methods rely on chemical cross-linking to stabilize spatial interactions. This step remains a "black box" as regards the biases it may introduce, and some discrepancies between microscopy and 3C studies have now been reported. To address these concerns, we developed "i3C", a novel approach for capturing spatial interactions without a need for cross-linking. We apply i3C to intact nuclei of living cells and exploit native forces that stabilize chromatin folding. Using different cell types and loci, computational modeling, and a methylation-based orthogonal validation method, "TALE-iD", we show that native interactions resemble cross-linked ones, but display improved signal-to-noise ratios and are more focal on regulatory elements and CTCF sites, while strictly abiding to topologically associating domain restrictions.
authors.affiliation: Center for Molecular Medicine, University of Cologne, Cologne, Germany.
authors.forename: Lilija
authors.initials: L
authors.lastname: Brant
authors.affiliation: Center for Molecular Medicine, University of Cologne, Cologne, Germany.
authors.forename: Theodore
authors.initials: T
authors.lastname: Georgomanolis
authors.affiliation: Center for Molecular Medicine, University of Cologne, Cologne, Germany.
authors.forename: Milos
authors.initials: M
authors.lastname: Nikolic
authors.affiliation: School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK.
authors.forename: Chris A
authors.initials: CA
authors.lastname: Brackley
authors.affiliation: Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands.
authors.forename: Petros
authors.initials: P
authors.lastname: Kolovos
authors.affiliation: Biomics Department, Erasmus Medical Center, Rotterdam, The Netherlands.
authors.forename: Wilfred
authors.identifier: http://orcid.org/0000-0002-0421-8301
authors.initials: W
authors.lastname: van Ijcken
authors.affiliation: Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands.
authors.forename: Frank G
authors.initials: FG
authors.lastname: Grosveld
authors.affiliation: School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK.
authors.forename: Davide
authors.initials: D
authors.lastname: Marenduzzo
authors.affiliation: Center for Molecular Medicine, University of Cologne, Cologne, Germany argyris.papantonis@uni-koeln.de.
authors.forename: Argyris
authors.identifier: http://orcid.org/0000-0001-7551-1073
authors.initials: A
authors.lastname: Papantonis
mesh_terms: D000818:Animals; D002467:Cell Nucleus / Q000235:genetics*; D002877:Chromosomes, Human / Q000737:chemistry* / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D061307:Human Umbilical Vein Endothelial Cells; D006801:Humans; D007399:Interphase; D020014:K562 Cells; D008322:Mammals / Q000235:genetics; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D017422:Sequence Analysis, DNA / Q000379:methods
keywords: chromatin looping; chromosome conformation capture; cross‐linking; nuclear compartments; nuclear organization