Introduction

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.

Publications

  1. Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts.
    Cite this
    Paulsen J, Sekelja M, Oldenburg AR, Barateau A, Briand N, Delbarre E, Shah A, Sørensen AL, Vigouroux C, Buendia B, Collas P, 2017-01-01 - Genome biology

Credits

  1. Jonas Paulsen
    Developer

    Department of Molecular Medicine, Institute of Basic Medical Sciences, Norway

  2. Monika Sekelja
    Developer

    Department of Molecular Medicine, Institute of Basic Medical Sciences, Norway

  3. Anja R Oldenburg
    Developer

    Department of Molecular Medicine, Institute of Basic Medical Sciences, Norway

  4. Alice Barateau
    Developer

    Institut BFA, Université Paris 7-CNRS, France

  5. Nolwenn Briand
    Developer

    Department of Molecular Medicine, Institute of Basic Medical Sciences, Norway

  6. Erwan Delbarre
    Developer

    Department of Molecular Medicine, Institute of Basic Medical Sciences, Norway

  7. Akshay Shah
    Developer

    Department of Molecular Medicine, Institute of Basic Medical Sciences, Norway

  8. Anita L Sørensen
    Developer

    Department of Molecular Medicine, Institute of Basic Medical Sciences, Norway

  9. Corinne Vigouroux
    Developer

    AP-HP Hôpital Tenon, Paris, France

  10. Brigitte Buendia
    Developer

    Institut BFA, Université Paris 7-CNRS, France

  11. Philippe Collas
    Investigator

    Norwegian Center for Stem Cell Research, Oslo University Hospital

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Summary
AccessionBT000021
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesPerl
User InterfaceTerminal Command Line
Download Count0
Submitted ByPhilippe Collas