Competition for a limited pool of cohesin between centromeres and the rDNA triggers chromosomal instability that shortens replicative lifespan

Sir2 is a highly conserved NAD+-dependent histone deacetylase that functions in heterochromatin formation and promotes replicative lifespan (RLS) in the budding yeast, Saccharomyces cerevisiae. Within the yeast rDNA locus, Sir2 is required for efficient cohesin recruitment and maintaining stability of the tandem array. In addition to the rDNA, ChIP-seq of an epitope-tagged cohesin subunit (Mcd1-13xMyc) in a sir2? mutant revealed subtle reductions of cohesin binding at all 16 centromeres. Coupled with the previously reported chromosome instability in sir2? cells and depletion of Sir2 in aged cells, we hypothesized that mitotic chromosome instability (CIN) due to Sir2 depletion could be a driver of replicative aging. In addition to Sir2, we discovered that other subunits of the Sir2-containing SIR and RENT complexes were depleted in aged cells, as were subunits of the cohesin and monopolin/cohibin complexes, implying the possibility of CIN. ChIP assays of the residual Mcd1-13xMyc in aged cells showed strong depletion from the rDNA and possible redistribution to centromeres, most likely in an attempt to maintain chromosome stability. Despite the shift in cohesin distribution, sister chromatid cohesion was partially attenuated in old cells and the frequency of chromosome loss was increased. This age-induced CIN was exacerbated in strains lacking Sir2 and its paralog, Hst1, but suppressed in strains that stabilize the rDNA array due to the deletion of FOB1 or through caloric restriction (CR). Furthermore, ectopic expression of MCD1 from a doxycycline-inducible promoter was sufficient to suppress to rDNA instability in aged cells and to extend RLS. Taken together we conclude that age-induced depletion of cohesin and multiple other nucleolar chromatin factors destabilize the rDNA locus, which then results in general CIN and aneuploidy that shortens RLS.