DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift

Franzen, Julia; Georgomanolis, Theodoros; Selich, Anton; Kuo, Chao-Chung; Stöger, Reinhard; Brant, Lilija; Mulabdić, Melita Sara; Fernandez-Rebollo, Eduardo; Grezella, Clara; Ostrowska, Alina; Begemann, Matthias; Nikolić, Miloš; Rath, Björn; Ho, Anthony D.; Rothe, Michael; Schambach, Axel; Papantonis, Argyris; Wagner, Wolfgang

Abstract

Culture expansion of primary cells evokes highly reproducible DNA methylation (DNAm) changes. We have identified CG dinucleotides (CpGs) that become continuously hyper- or hypomethylated during long-term culture of mesenchymal stem cells (MSCs) and other cell types. Bisulfite barcoded amplicon sequencing (BBA-seq) demonstrated that DNAm patterns of neighboring CpGs become more complex without evidence of continuous pattern development and without association to oligoclonal subpopulations. Circularized chromatin conformation capture (4C) revealed reproducible changes in nuclear organization between early and late passages, while there was no enriched interaction with other genomic regions that also harbor culture-associated DNAm changes. Chromatin immunoprecipitation of CTCF did not show significant differences during long-term culture of MSCs, however culture-associated hypermethylation was enriched at CTCF binding sites and hypomethylated CpGs were devoid of CTCF. Taken together, our results support the notion that DNAm changes during culture-expansion are not directly regulated by a targeted mechanism but rather resemble epigenetic drift.

Citation

Franzen, J., Georgomanolis, T., Selich, A., Kuo, C.-C., Stöger, R., Brant, L., Mulabdić, M. S., Fernandez-Rebollo, E., Grezella, C., Ostrowska, A., Begemann, M., Nikolić, M., Rath, B., Ho, A. D., Rothe, M., Schambach, A., Papantonis, A., & Wagner, W. (2021). DNA methylation changes during long-term in vitro cell culture are caused by epigenetic drift. Communications Biology, 4(1), Article 598. https://doi.org/10.1038/s42003-021-02116-y

• Journal Article Type: Article
• Acceptance Date: Apr 14, 2021
• Online Publication Date: May 19, 2021
• Publication Date: May 19, 2021
• Deposit Date: May 10, 2021
• Publicly Available Date: May 26, 2021
• Journal: Communications Biology
• Electronic ISSN: 2399-3642
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 4
• Issue: 1
• Article Number: 598
• DOI: https://doi.org/10.1038/s42003-021-02116-y
• Public URL: https://nottingham-repository.worktribe.com/output/5523115
• Publisher URL: https://www.nature.com/articles/s42003-021-02116-y