Chrom3D: Three-dimensional Genome Modeling from Hi-C and Nuclear Lamin-genome Contacts

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2017 Feb 1

PMID 28137286

Citations 116

Authors

Jonas Paulsen

Monika Sekelja

Anja R Oldenburg

Alice Barateau

Nolwenn Briand

Erwan Delbarre

Akshay Shah

Anita L Sorensen

Corinne Vigouroux

Brigitte Buendia

Philippe Collas

Affiliations

Soon will be listed here.

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.

Citing Articles

Effects of Lamina-Chromatin Attachment on Super Long-Range Chromatin Interactions.

Delafrouz P, Farooq H, Du L, Ma A, Liang J bioRxiv. 2025; .

PMID: 40027763 PMC: 11870427. DOI: 10.1101/2025.02.13.638183.

The Basis of Diversity in Laminopathy Phenotypes Caused by Variants in the Intron 8 Donor Splice Site of the Gene.

Shchagina O, Gilazova L, Filatova A, Vafina Z, Murtazina A, Chigvintceva P Int J Mol Sci. 2025; 26(3).

PMID: 39940784 PMC: 11818007. DOI: 10.3390/ijms26031015.

Cryo-EM structures of the BAF-Lamin A/C complex bound to nucleosomes.

Horikoshi N, Miyake R, Sogawa-Fujiwara C, Ogasawara M, Takizawa Y, Kurumizaka H Nat Commun. 2025; 16(1):1495.

PMID: 39929866 PMC: 11811190. DOI: 10.1038/s41467-025-56823-9.

Structural basis of differential gene expression at eQTLs loci from high-resolution ensemble models of 3D single-cell chromatin conformations.

Du L, Farooq H, Delafrouz P, Liang J Bioinformatics. 2025; 41(2).

PMID: 39891345 PMC: 11835231. DOI: 10.1093/bioinformatics/btaf050.

p53 Regulates Nuclear Architecture to Reduce Carcinogen Sensitivity and Mutagenic Potential.

King D, McCoy D, Perdyan A, Mieczkowski J, Douki T, Dionne J bioRxiv. 2024; .

PMID: 39345432 PMC: 11429700. DOI: 10.1101/2024.09.14.613067.

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