Break-induced replication: What is it and what is it for?

Llorente, Bertrand; Smith, Catherine E.; Symington, Lorraine S.

doi:10.4161/cc.7.7.5613

Cited by 265 publications

(267 citation statements)

References 35 publications

(47 reference statements)

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“…It is possible that this configuration offers alternative mechanisms for diploid cells to adjust the copy number of these genes through mitotic crossover, break-induced replication, or meiotic segregation followed by re-mating of sibling haploid spores (Paques and Haber 1999;Knop 2006;Llorente et al 2008). For example, these mechanisms could, in just a few generations, produce diploids containing 0 to 4 copies of MPR genes and 6 to 12 copies of SNO/ SNZ genes.…”

Section: Discussionmentioning

confidence: 99%

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Argueso

Carazzolle

Mieczkowski³

et al. 2009

Genome Res.

252

236

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Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. Here we report the molecular genetic analysis of a PE-2 derived diploid (JAY270), and the complete genome sequence of a haploid derivative (JAY291). The JAY270 genome is highly heterozygous (;2 SNPs/kb) and has several structural polymorphisms between homologous chromosomes. These chromosomal rearrangements are confined to the peripheral regions of the chromosomes, with breakpoints within repetitive DNA sequences. Despite its complex karyotype, this diploid, when sporulated, had a high frequency of viable spores. Hybrid diploids formed by outcrossing with the laboratory strain S288c also displayed good spore viability. Thus, the rearrangements that exist near the ends of chromosomes do not impair meiosis, as they do not span regions that contain essential genes. This observation is consistent with a model in which the peripheral regions of chromosomes represent plastic domains of the genome that are free to recombine ectopically and experiment with alternative structures. We also explored features of the JAY270 and JAY291 genomes that help explain their high adaptation to industrial environments, exhibiting desirable phenotypes such as high ethanol and cell mass production and high temperature and oxidative stress tolerance. The genomic manipulation of such strains could enable the creation of a new generation of industrial organisms, ideally suited for use as delivery vehicles for future bioenergy technologies.

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Section: Discussionmentioning

confidence: 99%

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Argueso

Carazzolle

Mieczkowski³

et al. 2009

Genome Res.

252

236

View full text Add to dashboard Cite

show abstract

“…These residual crossovers may reflect the activity of a yet-unidentified JM resolvase; they may also reflect the production of half-crossovers by breakinduced replication (Ho et al, 2010;Kogoma, 1996;Llorente et al, 2008) or by other mechanisms that do not involve dHJ-JM formation and resolution (Ivanov and Haber, 1995;Mazó n et al, 2012;Muñoz-Galván et al, 2012). Alternatively, long-tract NCO gene conversion events that include flanking heterologous sequences might be responsible for the products, scored in our molecular assays as COs, that are independent of both MutLg and SSNs.…”

Section: The Interplay Of Resolvase Activities Is Chromosome Context-mentioning

confidence: 99%

Local chromosome context is a major determinant of crossover pathway biochemistry during budding yeast meiosis

Medhi¹,

Goldman

Lichten³

2016

Preprint

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The budding yeast genome contains regions where meiotic recombination initiates more frequently than in others. This pattern parallels enrichment for the meiotic chromosome axis proteins Hop1 and Red1. These proteins are important for Spo11-catalyzed double strand break formation; their contribution to crossover recombination remains undefined. Using the sequencespecific VMA1-derived endonuclease (VDE) to initiate recombination in meiosis, we show that chromosome structure influences the choice of proteins that resolve recombination intermediates to form crossovers. At a Hop1-enriched locus, most VDE-initiated crossovers, like most Spo11-initiated crossovers, required the meiosis-specific MutLg resolvase. In contrast, at a locus with lower Hop1 occupancy, most VDE-initiated crossovers were MutLg-independent. In pch2 mutants, the two loci displayed similar Hop1 occupancy levels, and VDE-induced crossovers were similarly MutLg-dependent. We suggest that meiotic and mitotic recombination pathways coexist within meiotic cells, and that features of meiotic chromosome structure determine whether one or the other predominates in different regions.

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“…17,19,20 LTGC shares several properties with break-induced replication (BIR), a known mediator of genomic instability in yeast. [27][28][29][30][31] Indeed in BRCA1 mutant cells, LTGC is the most abundant HR product observed at Tus/Ter-stalled forks. Thus, determining the mechanisms underlying Tus/Ter-induced LTGC is crucial to understanding how the BRCA genes, and the HR machinery in general, suppress genomic instability at stalled replication forks.…”

Section: Introductionmentioning

confidence: 99%

Spatial separation of replisome arrest sites influences homologous recombination quality at a Tus/Ter-mediated replication fork barrier

Willis

Scully

2016

Cell Cycle

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The Escherichia coli replication fork arrest complex Tus/Ter mediates site-specific replication fork arrest and homologous recombination (HR) on a mammalian chromosome, inducing both conservative "short tract" gene conversion (STGC) and error-prone "long tract" gene conversion (LTGC) products. We showed previously that bidirectional fork arrest is required for the generation of STGC products at Tus/Ter-stalled replication forks and that the HR mediators BRCA1, BRCA2 and Rad51 mediate STGC but suppress LTGC at Tus/Ter-arrested forks. Here, we report the impact of Ter array length on Tus/Ter-induced HR, comparing HR reporters containing arrays of 6, 9, 15 or 21 Ter sites-each targeted to the ROSA26 locus of mouse embryonic stem (ES) cells. Increasing Ter copy number within the array beyond 6 did not affect the magnitude of Tus/Ter-induced HR but biased HR in favor of LTGC. A "lock"-defective Tus mutant, F140A, known to exhibit higher affinity than wild type (wt)Tus for duplex Ter, reproduced these effects. In contrast, increasing Ter copy number within the array reduced HR induced by the I-SceI homing endonuclease, but produced no consistent bias toward LTGC. Thus, the mechanisms governing HR at Tus/Ter-arrested replication forks are distinct from those governing HR at an enzyme-induced chromosomal double strand break (DSB). We propose that increased spatial separation of the 2 arrested forks encountering an extended Tus/Ter barrier impairs the coordination of DNA ends generated by the processing of the stalled forks, thereby favoring aberrant LTGC over conservative STGC.

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Break-induced replication: What is it and what is it for?

Cited by 265 publications

References 35 publications

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Local chromosome context is a major determinant of crossover pathway biochemistry during budding yeast meiosis

Spatial separation of replisome arrest sites influences homologous recombination quality at a Tus/Ter-mediated replication fork barrier

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