Be careful on DNA methylation alterations

Abstract

DNA methylation is an epigenetic modification involved in DNA compaction and in the regulation of gene expression. Also, DNA methylation is found in repetitive DNA including centromere and telomere. Recently, the research has been focused on repetitive sequences at the centromere due to its role in chromosome segregation, an event essential to cell fitness. So far, studies revealed that tumour cells are usually hypomethylated at repetitive sequences and that DNA hypomethylation leads to the loss of chromatid cohesion and to aneuploidy as well[1-2]. However, in the centromeric sequences there are no coding genes so it is still unclear what role DNA methylation plays in this context. In order to answer this question we used and compared immortalized (RPE-1) and tumour (DLD-1) cell lines, both engineered to allow an inducible DNA hypomethylation (in collaboration with Institut Curis, Paris). We took advantage of the Auxin Inducible Degron (AID) system[3] to degrade the endogenous AID-tagged DNMT1 (DNA-methyl- Transferase1). The induced DNMT1-AID degradation for several cell cycles leads to passive DNA hypomethylation. Our results showed that, once hypomethylated, immortalized non-tumour cells suffered a reduced growth rate. Both cell lines acquired aneuploidy and chromatids cohesion defects. We also observed an increase of mitotic errors, especially misaligned and lagging chromosomes, which strongly suggest a centromere/kinetochore malfunctioning. To this regard, by microscopy we noticed a reduced amount of centromeric proteins (CENPs) at centromere. Lastly, cells underwent nuclear and cytoskeleton defects that could also contribute to the genetic instability typical of tumour cells. In summary, our study reveals that methylation of repetitive DNA is indeed important to cells survival and fitness, probably by maintaining centromere stability and function and by impacting on nuclear/cytoskeleton mechanics. This also suggests cautiousness in the use of hypomethylating drug as anti-cancer therapy that may have a risky effect on normal cells.