Chromosome conformation of human fibroblasts grown in 3-dimensional spheroids

Nucleus
Haiming ChenIndika Rajapakse

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.

References

Jun 15, 1999·The Journal of Cell Biology·J A CroftW A Bickmore
Apr 4, 2002·Proceedings of the National Academy of Sciences of the United States of America·Hideyuki TanabeThomas Cremer
Sep 11, 2002·Trends in Cell Biology·Luis Parada, Tom Misteli
Oct 16, 2008·Cell·Takumi TakizawaTom Misteli
Sep 5, 2009·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Jacques RouquetteStanislav Fakan
Mar 20, 2010·Cold Spring Harbor Perspectives in Biology·Thomas Cremer, Marion Cremer
Oct 23, 2010·The Analyst·Yi-Chung TungShuichi Takayama
Mar 9, 2011·The Journal of Cell Biology·Indika Rajapakse, Mark Groudine
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Jun 2, 2012·Methods : a Companion to Methods in Enzymology·Jon-Matthew BeltonJob Dekker
Sep 4, 2012·Nature Methods·Maxim ImakaevLeonid A Mirny
Aug 12, 2014·Chromosoma·Nitasha SehgalRonald Berezney

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Citations

May 7, 2016·Bioinformatics·Jie ChenIndika Rajapakse
Dec 20, 2018·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Anna ZlotinaAlla Krasikova
Mar 5, 2017·Molecular Cancer Research : MCR·Laura SeamanIndika Rajapakse
Feb 26, 2021·Genomics, Proteomics & Bioinformatics·Xin LiuZhifeng Shao

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Methods Mentioned

BETA
Hi-C
ICE
PCR
pull-down

Software Mentioned

SAM
Bowtie2
analyzeHi
WIC
Hi
makeTagDirectory

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