Chromosome Conformation of Human Fibroblasts Grown in 3-Dimensional Spheroids

Abstract

In the study of interphase chromosome organization, genome-wide chromosome conformation capture (Hi-C) maps are often generated using 2-dimensional (2D) monolayer cultures. These 2D cells have morphological deviations from cells that exist in 3-dimensional (3D) tissues in vivo, and may not maintain the same chromosome conformation. We used Hi-C maps to test the extent of differences in chromosome conformation between human fibroblasts grown in 2D cultures and those grown in 3D spheroids. Significant differences in chromosome conformation were found between 2D cells and those grown in spheroids. Intra-chromosomal interactions were generally increased in spheroid cells, with a few exceptions, while inter-chromosomal interactions were generally decreased. Overall, chromosomes located closer to the nuclear periphery had increased intra-chromosomal contacts in spheroid cells, while those located more centrally had decreased interactions. This study highlights the necessity to conduct studies on the topography of the interphase nucleus under conditions that mimic an in vivo environment.

Keywords:

• chromatin
• chromosome conformation
• chromosome territories
• interphase nucleus
• 3-dimensional spheroids

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Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Acknowledgments

We thank Lindsey Muir and Joan Ritland Politz for critical reading of the manuscript. We also thanks Dr. Richard Mc Eachin for support in processing Illumina sequence data with a standardized pipeline, Walter Meixner for providing microscopy images obtained from 3D spheroids, and Laura Seaman for helpful discussion on the manuscript. We are grateful to Dr. Job Dekker for providing the Hi-C protocol.

Funding

This work is supported with a grant from Defense Advanced Research Projects Agency (DARPA) Biochronicity Project and National Institutes of Health (NIH; grant K25DK082791–01A109) to IR. The work of J. Chen and A. O. Hero was partially supported by Defense Advanced Research Projects Agency (DARPA), under the Predicting Health and Disease (PHD) program.

Supplementary Material

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