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

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• 作者：Jonas Paulsen ; Monika Sekelja ; Anja R. Oldenburg ; Alice Barateau…
• 关键词：Three ; dimensional (3D) genome ; Hi ; C ; Lamin ; associated domain (LAD) ; Laminopathy ; Modeling ; Nuclear lamin ; Topologically ; associated domain (TAD)
• 刊名：Genome Biology
• 出版年：2017
• 出版时间：December 2017
• 年：2017
• 卷：18
• 期：1
• 全文大小：1913KB
• 刊物主题：Animal Genetics and Genomics; Human Genetics; Plant Genetics & Genomics; Microbial Genetics and Genomics; Bioinformatics; Evolutionary Biology;
• 出版者：BioMed Central
• ISSN：1474-760X
• 卷排序：18

文摘

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.