Universität zu Köln

Brant, Lilija, Georgomanolis, Theodore, Nikolic, Milos ORCID: 0000-0003-0029-7601, Brackley, Chris A., Kolovos, Petros ORCID: 0000-0002-0787-6158, van Ijcken, Wilfred, Grosveld, Frank G., Marenduzzo, Davide ORCID: 0000-0003-3974-4915 and Papantonis, Argyris ORCID: 0000-0001-7551-1073 (2016). Exploiting native forces to capture chromosome conformation in mammalian cell nuclei. Mol. Syst. Biol., 12 (12). HOBOKEN: WILEY. ISSN 1744-4292

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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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Brant, Lilija UNSPECIFIED UNSPECIFIED UNSPECIFIED Georgomanolis, Theodore UNSPECIFIED UNSPECIFIED UNSPECIFIED Nikolic, Milos UNSPECIFIED orcid.org/0000-0003-0029-7601 UNSPECIFIED Brackley, Chris A. UNSPECIFIED UNSPECIFIED UNSPECIFIED Kolovos, Petros UNSPECIFIED orcid.org/0000-0002-0787-6158 UNSPECIFIED van Ijcken, Wilfred UNSPECIFIED UNSPECIFIED UNSPECIFIED Grosveld, Frank G. UNSPECIFIED UNSPECIFIED UNSPECIFIED Marenduzzo, Davide UNSPECIFIED orcid.org/0000-0003-3974-4915 UNSPECIFIED Papantonis, Argyris UNSPECIFIED orcid.org/0000-0001-7551-1073 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-253336
DOI:	10.15252/msb.20167311
Journal or Publication Title:	Mol. Syst. Biol.
Volume:	12
Number:	12
Date:	2016
Publisher:	WILEY
Place of Publication:	HOBOKEN
ISSN:	1744-4292
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language FORMALDEHYDE CROSS-LINKING; CHROMATIN INTERACTIONS; TOPOLOGICAL DOMAINS; REGULATORY REGIONS; GENOME; ORGANIZATION; FACTORIES; REVEALS; GENES; LOCUS Multiple languages Biochemistry & Molecular Biology Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/25333