title: Formation of Extrachromosomal Circular DNA from Long Terminal Repeats of Retrotransposons in Saccharomyces cerevisiae.
abstract: 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 extrachromosomal linear DNA during the transpositional life cycle of retrotransposons, or from circularization of genomic Ty DNA. Circularization may happen through nonhomologous end-joining (NHEJ) of long terminal repeats (LTRs) flanking Ty elements, 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 NHEJ 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 an RNA intermediate directly through DNA circularization.
authors.affiliation: Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
authors.forename: Henrik D
authors.initials: HD
authors.lastname: Møller
authors.affiliation: Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
authors.forename: Camilla E
authors.initials: CE
authors.lastname: Larsen
authors.affiliation: Lewis-Sigler Institute for Integrative Genomics, Princeton University, New Jersey 08544.
authors.forename: Lance
authors.initials: L
authors.lastname: Parsons
authors.affiliation: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark.
authors.forename: Anders Johannes
authors.initials: AJ
authors.lastname: Hansen
authors.affiliation: Department of Biology, University of Copenhagen, DK-2200 Copenhagen N, Denmark.
authors.forename: Birgitte
authors.initials: B
authors.lastname: Regenberg
authors.affiliation: Center for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK-1350 Copenhagen K, Denmark tmourier@snm.ku.dk.
authors.forename: Tobias
authors.initials: T
authors.lastname: Mourier
mesh_terms: D001483:Base Sequence; D056905:Chromosome Breakpoints; D004270:DNA, Circular; D004271:DNA, Fungal; D019143:Evolution, Molecular; D008969:Molecular Sequence Data; D005810:Multigene Family; D010957:Plasmids; D011995:Recombination, Genetic; D018626:Retroelements; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D016415:Sequence Alignment; D020079:Terminal Repeat Sequences
chemical_list: D004270:DNA, Circular; D004271:DNA, Fungal; D018626:Retroelements
keywords: circular DNA; long terminal repeats; recombination; transposable elements; yeast