title: Segmental duplications arise from Pol32-dependent repair of broken forks through two alternative replication-based mechanisms.
abstract: The propensity of segmental duplications (SDs) to promote genomic instability is of increasing interest since their involvement in numerous human genomic diseases and cancers was revealed. However, the mechanism(s) responsible for their appearance remain mostly speculative. Here, we show that in budding yeast, replication accidents, which are most likely transformed into broken forks, play a causal role in the formation of SDs. The Pol32 subunit of the major replicative polymerase Poldelta is required for all SD formation, demonstrating that SDs result from untimely DNA synthesis rather than from unequal crossing-over. Although Pol32 is known to be required for classical (Rad52-dependant) break-induced replication, only half of the SDs can be attributed to this mechanism. The remaining SDs are generated through a Rad52-independent mechanism of template switching between microsatellites or microhomologous sequences. This new mechanism, named microhomology/microsatellite-induced replication (MMIR), differs from all known DNA double-strand break repair pathways, as MMIR-mediated duplications still occur in the combined absence of homologous recombination, microhomology-mediated, and nonhomologous end joining machineries. The interplay between these two replication-based pathways explains important features of higher eukaryotic genomes, such as the strong, but not strict, association between SDs and transposable elements, as well as the frequent formation of oncogenic fusion genes generating protein innovations at SD junctions.
authors.affiliation: Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS, URA2171, Université Pierre et Marie Curie-Paris 6, UFR927, Paris, France.
authors.forename: Celia
authors.initials: C
authors.lastname: Payen
authors.forename: Romain
authors.initials: R
authors.lastname: Koszul
authors.forename: Bernard
authors.initials: B
authors.lastname: Dujon
authors.forename: Gilles
authors.initials: G
authors.lastname: Fischer
mesh_terms: D001483:Base Sequence; D053903:DNA Breaks, Double-Stranded; D004260:DNA Repair / Q000235:genetics / Q000502:physiology*; D045643:DNA Repair Enzymes; D004261:DNA Replication / Q000502:physiology*; D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins / Q000378:metabolism; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism*; D004720:Endonucleases / Q000378:metabolism; D020440:Gene Duplication; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D015719:Single-Strand Specific DNA and RNA Endonucleases
chemical_list: D004251:DNA Transposable Elements; D004268:DNA-Binding Proteins; C522758:Pol32 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D004259:DNA-Directed DNA Polymerase; D004720:Endonucleases; C069266:RAD1 protein, S cerevisiae; C064162:RAD10 protein, S cerevisiae; D015719:Single-Strand Specific DNA and RNA Endonucleases; D045643:DNA Repair Enzymes
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