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Genome Biol. 2017 Jan 30;18(1):21. doi: 10.1186/s13059-016-1146-2.

Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts.

Author information

1
Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
2
Institut BFA, Université Paris 7-CNRS, Paris, France.
3
INSERM, UMR S938, Centre de Recherches Saint-Antoine, Paris, France.
4
UPMC Université Paris 6 UMR S938, Paris, France.
5
ICAN, Paris, France.
6
AP-HP Hôpital Tenon, Paris, France.
7
Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway. philc@medisin.uio.no.
8
Norwegian Center for Stem Cell Research, Oslo University Hospital, Oslo, Norway. philc@medisin.uio.no.

Abstract

Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational modeling framework that simulates positions of topologically-associated domains (TADs) relative to each other and to the nuclear periphery. Chrom3D integrates chromosome conformation capture (Hi-C) and lamin-associated domain (LAD) datasets to generate structure ensembles that recapitulate radial distributions of TADs detected in single cells. Chrom3D reveals unexpected spatial features of LAD regulation in cells from patients with a laminopathy-causing lamin mutation. Chrom3D is freely available on github.

KEYWORDS:

Hi-C; Lamin-associated domain (LAD); Laminopathy; Modeling; Nuclear lamin; Three-dimensional (3D) genome; Topologically-associated domain (TAD)

PMID:
28137286
PMCID:
PMC5278575
DOI:
10.1186/s13059-016-1146-2
[Indexed for MEDLINE]
Free PMC Article

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