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Chromosome conformation and gene expression patterns differ profoundly in human fibroblasts grown in spheroids versus monolayers.

ABSTRACT: Human cells derived for in vitro cultures are conventionally grown as adherent monolayers (2D) which do not resemble natural 3 dimensional (3D) tissue architecture. We examined genome structure with chromosome conformation capture (Hi-C) and gene expression with RNA-seq in fibroblasts derived from human foreskin grown in 2D and 3D conditions. Our combined analysis of Hi-C and RNA-seq data shows a large number of differentially expressed genes between 2D and 3D cells, and these changes are localized in genomic regions that displayed structural changes. We also find a trend of expression in a subset of skin-specific genes in fibroblast cells grown in 3D that resembles those in native tissue.

SUBMITTER: Chen H

PROVIDER: S-EPMC5597289 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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Chromosome conformation and gene expression patterns differ profoundly in human fibroblasts grown in spheroids versus monolayers.

Chen Haiming H Seaman Laura L Liu Sijia S Ried Thomas T Rajapakse Indika I

Nucleus (Austin, Tex.) 20170127 4

Human cells derived for in vitro cultures are conventionally grown as adherent monolayers (2D) which do not resemble natural 3 dimensional (3D) tissue architecture. We examined genome structure with chromosome conformation capture (Hi-C) and gene expression with RNA-seq in fibroblasts derived from human foreskin grown in 2D and 3D conditions. Our combined analysis of Hi-C and RNA-seq data shows a large number of differentially expressed genes between 2D and 3D cells, and these changes are locali ...[more]

PMID: 28129029

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Chromosome conformation of human fibroblasts grown in 3-dimensional spheroids.

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Do Temporal Eating Patterns Differ in Healthy versus Unhealthy Overweight/Obese Individuals?

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The Reason Matters: Deep Wrist Injury Patterns Differ with Intentionality (Accident versus Suicide Attempt).

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