Reshuffling yeast chromosomes with CRISPR/Cas9

Fleiss, Aubin; O’Donnell, Samuel; Fournier, Téo; Lü, Wenqing; Agier, Nicolas; Delmas, Stéphane; Schacherer, Joseph; Fischer, Gilles

doi:10.1371/journal.pgen.1008332

Cited by 62 publications

(63 citation statements)

References 68 publications

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“…In all of these studies, multiple copies of Ty elements were found to be involved in the generation of translocations. In the study that employed CRISPR, similar multiple translocation events were observed (61). However, Ty elements in S. cerevisiae are distributed across the genome, unlike C. neoformans, where all of the Tcn2 elements are clustered in centromeres.…”

Section: Discussionmentioning

confidence: 62%

See 1 more Smart Citation

Centromere scission drives chromosome shuffling and reproductive isolation

Yadav

Sun

Coelho

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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A fundamental characteristic of eukaryotic organisms is the generation of genetic variation via sexual reproduction. Conversely, significant large-scale genome structure variations could hamper sexual reproduction, causing reproductive isolation and promoting speciation. The underlying processes behind large-scale genome rearrangements are not well understood and include chromosome translocations involving centromeres. Recent genomic studies in theCryptococcusspecies complex revealed that chromosome translocations generated via centromere recombination have reshaped the genomes of different species. In this study, multiple DNA double-strand breaks (DSBs) were generated via the CRISPR/Cas9 system at centromere-specific retrotransposons in the human fungal pathogenCryptococcus neoformans. The resulting DSBs were repaired in a complex manner, leading to the formation of multiple interchromosomal rearrangements and new telomeres, similar to chromothripsis-like events. The newly generated strains harboring chromosome translocations exhibited normal vegetative growth but failed to undergo successful sexual reproduction with the parental wild-type strain. One of these strains failed to produce any spores, while another produced ∼3% viable progeny. The germinated progeny exhibited aneuploidy for multiple chromosomes and showed improved fertility with both parents. All chromosome translocation events were accompanied without any detectable change in gene sequences and thus suggest that chromosomal translocations alone may play an underappreciated role in the onset of reproductive isolation and speciation.

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Section: Discussionmentioning

confidence: 62%

“…cerevisiae, where DSBs were generated with gamma radiation, HO-endonuclease, or CRISPR (60)(61)(62). In all of these studies, multiple copies of Ty elements were found to be involved in the generation of translocations.…”

Section: Discussionmentioning

confidence: 99%

Centromere scission drives chromosome shuffling and reproductive isolation

Yadav

Sun

Coelho

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…The impact of translocations in the phenotypic adaptation of yeast has been widely investigated by using genetically engineered strains (Tosato and Bruschi, 2015; Fleiss et al, 2019). However, the description of spontaneous chromosomal rearrangements in clonal populations is much less described.…”

Section: Resultsmentioning

confidence: 99%

TheSSU1checkup, a rapid tool for detecting chromosomal rearrangements of theSaccharomyces cerevisiaechromosome XVI. An ecological and technological study on wine yeast

Marullo

Claisse

Eder

et al. 2020

Preprint

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1)AbstractChromosomal rearrangements (CR) such as translocations, duplications and inversions play a decisive role in the adaptation of microorganisms to specific environments. In enological Saccharomyces cerevisiae strains, CR involving the promoter region of the gene SSU1 lead to a higher sulfite tolerance by enhancing the SO2 efflux. To date, three different SSU1 associated CR events have been described, including translocations XV-t-XVI and VIII-t-XVI and inversion inv-XVI. In the present study, we developed a multiplex PCR method (SSU1 check-up) that allows a rapid characterization of these three chromosomal configurations in a single experiment. Nearly 600 S. cerevisiae strains collected from fermented grape juice were genotyped by microsatellite markers. We demonstrated that alleles of the SSU1 promoter are differently distributed according to the wine environment (cellar versus vineyard) and the nature of the grape juice. Moreover, rearranged SSU1 promoters are significantly enriched among commercial starters. In addition, nearly isogenic strains collected in similar environments show different CR suggesting that translocation events occur with a non-negligible frequency in clonal populations likely due to mitotic recombination events. Finally, the link between the nature of SSU1 promoter and the tolerance to sulfite was statistically validated in natural grape juice containing various SO2 concentrations. The SSU1 check-up is therefore a convenient new tool for addressing population genetics questions and for selecting yeast strains by using molecular markers.

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“…Examples of using CRISPR/Cas9 to engineer chromosome rearrangements in other model systems include the creation of an oncogenic translocation in mice (5), translocations in yeast (6), translocations and inversions in C. elegans (7,8), and inversions in zebrafish (9). This study represents the first report of a chromosomal rearrangement induced by CRISPR/Cas9 in the Drosophila germline.…”

Section: Introductionmentioning

confidence: 91%

A method to estimate the frequency of chromosomal rearrangements induced by CRISPR/Cas9 multiplexing in Drosophila

Reed

2019

Preprint

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Using CRISPR/Cas9 to simultaneously induce mutations in two or more target genes, commonly referred to as multiplexing, may result in chromosomal rearrangements such as inversions or translocations. While this may be undesirable in some contexts, the ability to recover chromosomal rearrangements targeted to specific sites in the genome is potentially a powerful tool. Before developing such tools, however, it is first important to measure the frequency with which chromosome rearrangements are induced by CRISPR/Cas9 multiplexing. To do this, we have developed a selfselecting screening system using a Drosophila line that carries an autosomal pericentric inversion in what is known as the autosynaptic form. All progeny of normal females crossed to males of this autosynaptic stock are lethal due to excessive aneuploidy. If an inversion is induced within the female germline, and if it is analogous to the inversion in the male autosynaptic line, then it is possible to recover progeny in which aneuploidy is reduced and viability is restored. Using this selfselection method, we screened 130 females and recovered one new autosynaptic element. Salivary gland polytene chromosome analysis, PCR, and sequencing confirmed the recovery of a breakpoint induced precisely between the two sgRNA target sites. Overall, we demonstrate that CRISPR/Cas9 multiplexing can induce chromosomal rearrangements in Drosophila. Also, in using this particular system, the recovery of chromosomal rearrangements was not a high frequency event.

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Reshuffling yeast chromosomes with CRISPR/Cas9

Cited by 62 publications

References 68 publications

Centromere scission drives chromosome shuffling and reproductive isolation

Centromere scission drives chromosome shuffling and reproductive isolation

TheSSU1checkup, a rapid tool for detecting chromosomal rearrangements of theSaccharomyces cerevisiaechromosome XVI. An ecological and technological study on wine yeast

A method to estimate the frequency of chromosomal rearrangements induced by CRISPR/Cas9 multiplexing in Drosophila

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