EccDNA preparation from biological B02-B05 samples. Each sample from 1x10^6 cells.

Extrachromosomal circular DNA (eccDNA) derived from chromosomal Ty retrotransposons in yeast can be generated in multiple ways. Ty eccDNA can arise from the circularization of extra-chromosomal linear DNA during the transpositional life cycle of retrotransposons or from circularization of genomic Ty DNA. Mechanisms of circularization may happen through non-homologous end-joining (NHEJ) of long terminal repeats (LTRs) flanking Ty’s, by Ty autointegration, or by LTR-LTR recombination. By performing an in-depth investigation of sequence reads stemming from Ty eccDNAs obtained from populations of Saccharomyces cerevisiae S288c, we find that eccDNAs predominantly correspond to full-length Ty1 elements. Analyses of sequence junctions reveal no signs of non-homologous end-joining or autointegration events. We detect recombination junctions that are consistent with yeast Ty eccDNAs being generated through recombination events within the genome. This opens the possibility that retrotransposable elements could move around in the genome without a RNA intermediate but directly through DNA circularization.