ERC accumulation depletes Sir2 from rDNA and induces cellular senescence by rDNA destabilization

Genome instability is a major factor contributing to cellular senescence. The rRNA gene (rDNA), a repetitive sequence array, is a highly unstable region of the genome. In budding yeast, this instability induces senescence and shortens the lifespan. While the importance of rDNA stability in the aging process is well recognized, the mechanism driving rDNA instability in old cells remains unclear. Using effective methods to isolate old cells in budding yeast, our observations suggest that non-coding RNA transcription from the bidirectional promoter E-pro increases by acetylation of histones H3K14 and H4K16, thereby triggering rDNA instability in old cells. Depletion of Gcn5, the enzyme responsible for H3K14 acetylation, reduced E-pro transcription and mitigated rDNA instability in old cells. Contrary to previous studies, the level of Sir2, a deacetylase for H3K14 and H4K16, does not decline with aging. However, acetylation levels at the E-pro region increase, promoting non-coding RNA transcription and rDNA instability in old cells. This phenomenon appears to be driven by Sir2 depletion from chromosomal rDNA, caused by the accumulation of extrachromosomal rDNA circles (ERCs). We propose a new model of cellular senescence in budding yeast, driven by Sir2 depletion and rDNA instability.