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

• Published in: Genome Biology Vol. 18; no. 1; p. 21
• Main Authors: Paulsen, Jonas, Sekelja, Monika, Oldenburg, Anja R, Barateau, Alice, Briand, Nolwenn, Delbarre, Erwan, Shah, Akshay, Sørensen, Anita L, Vigouroux, Corinne, Buendia, Brigitte, Collas, Philippe
• Format: Journal Article
• Language: English
• Published: England BioMed Central 30-01-2017
• Subjects: Adult; Biochemistry, Molecular Biology; Chromatin - genetics; Chromosomes; Computational Biology - methods; Computer applications; Conformation; Female; Gene expression; Genome; Genomes; Genomics; HeLa Cells; Humans; Life Sciences; Male; Mammals; Metabolism; Method; Models, Genetic; Nuclear Lamina - genetics; Young Adult; Hi-C; Laminopathy; Three-dimensional (3D) genome; Lamin-associated domain (LAD); Modeling; Nuclear lamin; Topologically-associated domain (TAD)
• ISSN: 1474-760X; 1474-7596; 1465-6906; 1474-760X
• DOI: 10.1186/s13059-016-1146-2

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.