DNA hypomethylation leads to chromosomal instability, along with structural and mechanical defects of the nucleus

Background DNA methylation is an epigenetic modification that promotes chromatin condensation, regulating both chromatin structure and gene transcription. Global loss of DNA methylation occurring at gene-poor repetitive sequences - the most abundant elements of the genome - is a hallmark of genomic instability and several human diseases, notably cancer. Beyond transcriptional regulation, DNA methylation plays a crucial role in maintaining repetitive sequences in a heterochromatic, compacted state. To this regard, heterochromatin has a specific organization and positioning within the nucleus, and together with the nuclear lamina contributes to regulating nuclear stiffness. Hence, global DNA hypomethylation, by affecting heterochromatin, could impact both nuclear architecture and mechanical properties. This study explores this connection and proposes a novel mechanism by which DNA hypomethylation contributes to genomic instability and tumor formation. Results Our study employs the non-tumor immortalized RPE-1 cell line, engineered to induce DNA hypomethylation. Upon hypomethylation, cells acquire aneuploidy and accumulate mitotic defects, suggesting the crucial role of DNA methylation in supporting chromosome segregation. Moreover, microscopy analyses revealed that DNA hypomethylation induces distinct nuclear phenotypic changes, including nuclear enlargement and increased blebbing. These alterations are associated with changes in nuclear envelope composition, as evidenced by reduced levels and impaired localization of key nuclear proteins (LaminB1 and LBR), likely weakening nuclear envelope structural integrity. Lastly, biophysical approaches showed that DNA hypomethylation correlates with decreased nuclear membrane tension and reduced nuclear stiffness, which may lead to increased nuclear plasticity. Conclusions Altogether, these findings suggest that DNA hypomethylation could undermine chromosome segregation and disrupt nuclear envelope integrity, leading to structural and mechanical defects that alter nuclear deformability, potentially promoting cell transformation. Overall, this research provides new insights into the role of DNA methylation in preserving genome stability by maintaining nuclear architecture and mechanical properties, proposing DNA hypomethylation as a potential oncogenic event.