title: Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts.
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.
authors.affiliation: Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
authors.forename: Jonas
authors.initials: J
authors.lastname: Paulsen
authors.affiliation: Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
authors.forename: Monika
authors.initials: M
authors.lastname: Sekelja
authors.affiliation: Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
authors.forename: Anja R
authors.initials: AR
authors.lastname: Oldenburg
authors.affiliation: Institut BFA, Université Paris 7-CNRS, Paris, France.
authors.forename: Alice
authors.initials: A
authors.lastname: Barateau
authors.affiliation: Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
authors.forename: Nolwenn
authors.initials: N
authors.lastname: Briand
authors.affiliation: Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
authors.forename: Erwan
authors.initials: E
authors.lastname: Delbarre
authors.affiliation: Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
authors.forename: Akshay
authors.initials: A
authors.lastname: Shah
authors.affiliation: Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
authors.forename: Anita L
authors.initials: AL
authors.lastname: Sørensen
authors.affiliation: INSERM, UMR S938, Centre de Recherches Saint-Antoine, Paris, France.|UPMC Université Paris 6 UMR S938, Paris, France.|ICAN, Paris, France.|AP-HP Hôpital Tenon, Paris, France.
authors.forename: Corinne
authors.initials: C
authors.lastname: Vigouroux
authors.affiliation: Institut BFA, Université Paris 7-CNRS, Paris, France.
authors.forename: Brigitte
authors.initials: B
authors.lastname: Buendia
authors.affiliation: Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway. philc@medisin.uio.no.|Norwegian Center for Stem Cell Research, Oslo University Hospital, Oslo, Norway. philc@medisin.uio.no.
authors.forename: Philippe
authors.initials: P
authors.lastname: Collas
mesh_terms: D000328:Adult; D002843:Chromatin / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D005260:Female; D016678:Genome; D006367:HeLa Cells; D006801:Humans; D008297:Male; D008957:Models, Genetic; D034881:Nuclear Lamina / Q000235:genetics*; D055815:Young Adult
chemical_list: D002843:Chromatin
keywords: Hi-C; Lamin-associated domain (LAD); Laminopathy; Modeling; Nuclear lamin; Three-dimensional (3D) genome; Topologically-associated domain (TAD)