Template switching between the leading and lagging strands at replication forks generates inverted copy number variants through hairpin-capped extrachromosomal DNA
Fig 1
Comparison of “dogbone” and “hairpin” ODIRA models for inverted triplication of the SUL1 locus.
In the following diagrams thick lines indicate double stranded duplexes and thin lines indicate individual single strands. A) In our ODIRA model we propose that stalled forks (2a) provide an opportunity for a template switch between the nascent leading strand and the lagging strand template that occurs at short, interrupted inverted repeats (2b). Extension of the displaced leading strand and its ligation to an Okazaki fragment (2c) results in a covalent linkage between the leading and lagging nascent strands that can be expelled from the chromosome by an incoming fork from an adjacent origin (2d, and 3). A similar template switch at the divergent fork results in an extrachromosomal, self-complementary, single-stranded circular molecule (dogbone; 3). In the next cell cycle, the dogbone can replicate from its resident origin creating a duplex circular molecule that has two copies of the SUL1 region in inverted orientation (4). Recombination of the inverted dimeric circular molecule into the chromosome through homology with the SUL1 region creates a triplication with the center copy in inverted orientation (5). The inversion junctions (Cen-proximal and Tel-proximal; CJ and TJ, respectively) map to the genomic, short interrupted, inverted repeats where the template switching occurred. B) The Cen-proximal and Tel-proximal inversions can occur in different cell cycles, generating inverted linear molecules. After the second, telomere-proximal junction is created, the doubly inverted linear molecule can recombine with the SUL1 region creating an inverted triplication that is identical to that produced by the dogbone ODIRA model. The gray shaded panels in A and B show both strands of the DNA as thin lines to highlight the mechanism of template switches and the expelled transient intermediates (dogbones and hairpins). The dotted rectangles indicate the final chromosomal products of the two pathways.