Formation of Extrachromosomal Circular DNA from Long Terminal Repeats of Retrotransposons inSaccharomyces 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.

Transposable elements and circular DNAs

“…In summary, we have previously shown that circular DNAs are generated from genomic copies of yeast transposable elements 7 . It is currently unknown to which extent this is happening in mammalian genomes rich in transposable element sequences.…”

“…If nucleotide differences exist between the 2 LTR sequences flanking an element the apparent breakpoint site can be inferred, 5 and any apparent breakpoints outside the transcription start site region are therefore inconsistent with circles generated through circularization of linear extra-chromosomal DNA. Although only a few LTR sequences contained informative nucleotide differences, all tested sequences were inconsistent with being generated through circularization of linear extra-chromosomal DNA 7 . It therefore seems that yeast LTR elements are a source for circular DNAs through genomic recombination between the flanking LTR sequences.…”

“…In this respect, the multitude and sequence redundancy of transposable elements should render them highly efficient agents for the generation of circular DNAs. We recently assessed the involvement of transposable elements in the genesis of circular DNAs in baker's yeast, Saccharomyces cerevisiae 7 . Detection of structural variants—of which circular DNAs are a subset—requires customized analysis and is not directly elucidated using conventional mapping of short sequence reads onto reference genomes 3,7 .…”

“…Most copies exist as solo LTR sequences, 12 presumably generated through recombination events 11 . When sequence reads highly enriched for circular sequences 3,13 were mapped onto the yeast genome, a relative uniform coverage was observed across full-length LTR elements and this level of coverage did not extend outside the LTR borders 7 . This suggested that the majority of LTR sequences in circular DNAs exist as full-length LTR elements, although circles generated from LTR sequences residing at different genomic location have also been reported 3,14,15 …”

“…Circularization of linear extra-chromosomal LTR DNAs can happen in several ways, including nonhomologous end-joining, recombination between flanking LTR sequences, and through so-called auto-integration in which the LTR element inserts into its own sequence 16,18,19 . However, due to the fact that these scenarios are all preceded by transcription of the genomic LTR element, any resulting circular LTR sequence will display an apparent breakpoint at the transcription start site (despite the fact that they may not be created by recombination events) 7,20 . If nucleotide differences exist between the 2 LTR sequences flanking an element the apparent breakpoint site can be inferred, 5 and any apparent breakpoints outside the transcription start site region are therefore inconsistent with circles generated through circularization of linear extra-chromosomal DNA.…”