Numerous human cancer types are caused by copy-number variations (CNVs) of proto-oncogenes. Yet, detecting chromosomal CNVs before they reach establishment in large cell populations is a major challenge. By screening for a potential deletion-byproduct of CNVs, the so-called extrachromosomal circular DNA (eccDNA), we reasoned that we might elucidate some of the early ongoing processes in genomic rearrangements.
To explore the existence of circular DNA in eukaryotes we have developed a highly-sensitive eccDNA purification method, Circle-Seq, that relies on removal of linear DNA and next-generation sequencing of circular DNA. We reveal that CNVs, in the form of eccDNAs, are common in the budding yeast Saccharomyces cerevisiae. More than a thousand different eccDNAs larger than 1 kb were recorded in the S288c strain background increasing the known number of eccDNA more than a hundred fold. A number of eccDNAs were found repeatedly in S288c and in the CEN.PK strain background, suggesting conserved hotspots for DNA circularization, e.g. at ribosomal RNA genes, glucose transporter genes HXT6, HXT7, metallothionein genes CUP1-1, CUP1-2, Ty-retrotranposons and Y’-telomeric genes. Recording of HXT6-HXT7 geneotypes indicated selection for [HXT6/7circles] in continued yeast cultures under glucose-limitation and [HXT6/7circles] also appeared to serve as intermediates of chromosomal amplifications. Sequenced recombination junctions of circular Ty-elements revealed that retrotransposons can form by recombination both within the genome and during the classical retrotranspositional life cycle.
Our results suggest that eccDNAs are frequent genomic rearrangements in S. cerevisiae that lead to deletions and transient gene amplifications. Consequently, S. cerevisiae is a useful model organism for studying the molecular basis and evolutionary consequences of eccDNA.