Global sequencing of circular DNA reveals loss of genetic variation and an essential role of replication origins for maintenance of circular DNA in aging yeast cells

Circular DNA of chromosomal origin is a much overlooked group of genomic structural variants. To investigate the fate of circular DNA in aging cells, we purified circular DNA from 8 populations of young cells and their aged descendants and sequenced their circular DNA. We obtained a robust mapping of circular DNA by aligning reads probabilistically to the yeast genome and quantified circular DNA through internal plasmid controls. Our results reveal that young cells in average have 62 different circular DNA per 10⁶ cells. Most circular DNA are lost as cells divide and only 6.3% are retained in cells as they age. Circles present in both young and old are characterized by replication origins, suggesting that this element is essential for retention. Among circles that persist as cells age are telomeric Y’ circles, rDNA circles and circles formed from low copy repeat regions such as the hexose transporter genes HXT6 and HXT7. The number of different circular DNA is higher in young cells than old cells, but old cells have an overall higher copy number level of circular DNA caused by accumulation of rDNA circles (log2 Fold-Change = 6.88 ± 4.02). In conclusion, our results show that cells loose circular DNA genetic heterogeneity and accumulate telomeric and rDNA circles as they age.