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; Fernández-Rebollo, Eduardo; Grezella, Clara; Ostrowska, Alina; Begemann, Matthias; Nikolić, Miloš; Rath, Björn; Ho, Anthony D.; Rothe, Michael; Schambach, Axel; Papantonis, Argyris; Wagner, Wolfgang

doi:10.1038/s42003-021-02116-y

Cited by 31 publications

(31 citation statements)

References 59 publications

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“…Immortalized cells are then grown further to homogenize telomere length across chromosome ends (92 ends) with hTERT removed at various time points (reported by black triangle, Fig.1A) to generate isogenic clones with controlled telomere length. Importantly, all cells roughly spend the same time in culture, thus minimizing effects imputable to cell culture conditions 34,35 . We applied this strategy to fibroblasts, myoblasts and their differentiated counterpart, myotubes.…”

Section: Resultsmentioning

confidence: 99%

“…1A) to generate isogenic clones with controlled telomere length. Importantly, all cells roughly spend the same time in culture, thus minimizing effects imputable to cell culture conditions 34,35 . We applied this strategy to fibroblasts, myoblasts and their differentiated counterpart, myotubes.…”

Section: Changes In Methylation But Not Transcription Is Enriched At ...mentioning

confidence: 99%

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Telomere Position Effect Over Long Distance acts as a genome-wide epigenetic regulator through a commoncis- element

Chevalier

Pienkwoski

Caron

et al. 2022

Preprint

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Among epigenetic modifiers, telomeres, represent attractive modulators of the genome in part through position effects. Telomere Position Effect Over Long Distances (TPE-OLD) modulates genes expression by changes in telomere-dependent long-distance loops, with a reach of 10Mb from a telomere. However, TPE-OLD remains poorly defined. To gain further insights into the genome-wide impact of telomere length on genomic and epigenomic regulation through TPE-OLD, we used cells with controlled telomere length combined to a genome wide transcriptome and methylome analysis. By integrating omics data, we identified a common cis-acting motif that behaves as an insulator or enhancer. Using reporter assays integrating this element, we uncovered the trans partners regulating this activity. Further exploiting our cellular model, we observed the depletion of one candidate factor, RBPJ, at TPE-OLD associated loci upon telomere shortening. We concluded that, at the genome-wide level, TPE-OLD is relayed by RBPJ binding Alu-like elements to telomeres that acts as enhancers. In response to external stimuli (i.e., Aging), TPE-OLD might act by coordinating telomere length to the action of Alu newly evolved enhancers in association with RBPJ.

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Section: Resultsmentioning

confidence: 99%

Section: Changes In Methylation But Not Transcription Is Enriched At ...mentioning

confidence: 99%

Telomere Position Effect Over Long Distance acts as a genome-wide epigenetic regulator through a commoncis- element

Chevalier

Pienkwoski

Caron

et al. 2022

Preprint

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“…Both the single-cell resolution of the data, as well as the added transcriptomic layer, allowed us to quantify DNA methylation in precisely defined cell populations. Thus, with scNMT-seq, we have been able to free ourselves from the need for pure cell populations that rely on a large panel of excellent FACS surface markers, and from the need for cell culture systems known to alter DNA methylation (Antequera et al, 1990; Franzen et al, 2021). Nonetheless, single-cell multi-omics also introduced new challenges such as the sparsity of the data and the modest cell numbers that are currently achievable.…”

Section: Discussionmentioning

confidence: 99%

Single-cell triple-omics uncovers DNA methylation as key feature of stemness in the healthy and ischemic adult brain

Kremer

Cerrizuela

Shukairi

et al. 2022

Preprint

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Stem cells in the adult brain are specialized astrocytes capable of generating neurons and glial cells. While neural stem cells (NSCs) and common astrocytes have clearly distinct functions, they share highly similar transcriptome profiles. How stemness is molecularly encoded is therefore unclear. Here we use single-cell NMT-seq to simultaneously characterize the transcriptome, DNA methylome and chromatin accessibility of astrocytes and the NSC lineage in the healthy and ischemic brain. Our data reveal distinct methylation profiles associated with either astrocyte or stem cell function. Stemness is conferred by methylation of astrocyte genes and demethylation of neurogenic genes that are expressed only later. Surprisingly, ischemic injury unlocks the stemness-methylome in common astrocytes enabling generation of neuroblasts. Furthermore, we show that oligodendrocytes employ Tet-mediated demethylation to regulate expression of myelin-related genes, many of which are abnormally methylated in multiple sclerosis. Overall, we show that DNA methylation is a promising target for regenerative medicine.

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“…Moreover, long-term culture of primary cells in general may induce changes in DNA methylation ( 153 ). Therefore, when spermatogenesis is re-created in vitro , the epigenetic status has often been investigated to make sure that no aberrant epigenetic patterns are present in the in vitro -derived germ cells ( 100 , 101 ).…”

Section: Safetymentioning

confidence: 99%

Spermatogonial Stem Cell-Based Therapies: Taking Preclinical Research to the Next Level

et al. 2022

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Fertility preservation via biobanking of testicular tissue retrieved from testicular biopsies is now generally recommended for boys who need to undergo gonadotoxic treatment prior to the onset of puberty, as a source of spermatogonial stem cells (SSCs). SSCs have the potential of forming spermatids and may be used for therapeutic fertility approaches later in life. Although in the past 30 years many milestones have been reached to work towards SSC-based fertility restoration therapies, including transplantation of SSCs, grafting of testicular tissue and various in vitro and ex vivo spermatogenesis approaches, unfortunately, all these fertility therapies are still in a preclinical phase and not yet available for patients who have become infertile because of their treatment during childhood. Therefore, it is now time to take the preclinical research towards SSC-based therapy to the next level to resolve major issues that impede clinical implementation. This review gives an outline of the state of the art of the effectiveness and safety of fertility preservation and SSC-based therapies and addresses the hurdles that need to be taken for optimal progression towards actual clinical implementation of safe and effective SSC-based fertility treatments in the near future.

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

Cited by 31 publications

References 59 publications

Telomere Position Effect Over Long Distance acts as a genome-wide epigenetic regulator through a commoncis- element

Telomere Position Effect Over Long Distance acts as a genome-wide epigenetic regulator through a commoncis- element

Single-cell triple-omics uncovers DNA methylation as key feature of stemness in the healthy and ischemic adult brain

Spermatogonial Stem Cell-Based Therapies: Taking Preclinical Research to the Next Level

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