Analyzing the impact of extrachromosomal rDNA circles (ERCs) on the ageing yeast transcriptome

Here we analyzed the widespread disruption of gene expression that accompanies yeast ageing, and surprisingly observed that this is completely independent of ERCs. Furthermore, we could not find subsets of genes that are differentially regulated in the presence of ERCs. High throughput imaging showed that the accumulation of Tom70-GFP which accompanies the onset of cell division defects at the Senescence Entry Point (SEP) also correlated poorly to ERC abundance, but allowed determination of a gene expression signature for the SEP. This signature included overexpression of mRNA from the chromosome XII region between the rDNA and the telomere (ChrXIIr), which has been previously noted to amplify during ageing. Mother Enrichment Project (MEP) yeast were harvested at log phase or aged for 24 or 48 hours in YPD. Mother cells were purified, total RNA extracted and libraries processed using a NEBNext Ultra II directional RNAseq kit with poly(A)+ selection module.