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Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements.

Publication ,  Journal Article
Qi, L; Sui, Y; Tang, X-X; McGinty, RJ; Liang, X-Z; Dominska, M; Zhang, K; Mirkin, SM; Zheng, D-Q; Petes, TD
Published in: PLoS Genet
January 2023

Although homologous recombination between transposable elements can drive genomic evolution in yeast by facilitating chromosomal rearrangements, the details of the underlying mechanisms are not fully clarified. In the genome of the yeast Saccharomyces cerevisiae, the most common class of transposon is the retrotransposon Ty1. Here, we explored how Cas9-induced double-strand breaks (DSBs) directed to Ty1 elements produce genomic alterations in this yeast species. Following Cas9 induction, we observed a significant elevation of chromosome rearrangements such as deletions, duplications and translocations. In addition, we found elevated rates of mitotic recombination, resulting in loss of heterozygosity. Using Southern analysis coupled with short- and long-read DNA sequencing, we revealed important features of recombination induced in retrotransposons. Almost all of the chromosomal rearrangements reflect the repair of DSBs at Ty1 elements by non-allelic homologous recombination; clustered Ty elements were hotspots for chromosome rearrangements. In contrast, a large proportion (about three-fourths) of the allelic mitotic recombination events have breakpoints in unique sequences. Our analysis suggests that some of the latter events reflect extensive processing of the broken ends produced in the Ty element that extend into unique sequences resulting in break-induced replication. Finally, we found that haploid and diploid strain have different preferences for the pathways used to repair double-stranded DNA breaks. Our findings demonstrate the importance of DNA lesions in retrotransposons in driving genome evolution.

Duke Scholars

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Published In

PLoS Genet

DOI

EISSN

1553-7404

Publication Date

January 2023

Volume

19

Issue

1

Start / End Page

e1010590

Location

United States

Related Subject Headings

  • Saccharomyces cerevisiae
  • Retroelements
  • Humans
  • Homologous Recombination
  • Developmental Biology
  • DNA Breaks, Double-Stranded
  • Chromosome Aberrations
  • CRISPR-Cas Systems
  • 3105 Genetics
  • 0604 Genetics
 

Citation

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Qi, L., Sui, Y., Tang, X.-X., McGinty, R. J., Liang, X.-Z., Dominska, M., … Petes, T. D. (2023). Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements. PLoS Genet, 19(1), e1010590. https://doi.org/10.1371/journal.pgen.1010590
Qi, Lei, Yang Sui, Xing-Xing Tang, Ryan J. McGinty, Xiao-Zhuan Liang, Margaret Dominska, Ke Zhang, Sergei M. Mirkin, Dao-Qiong Zheng, and Thomas D. Petes. “Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements.PLoS Genet 19, no. 1 (January 2023): e1010590. https://doi.org/10.1371/journal.pgen.1010590.
Qi L, Sui Y, Tang X-X, McGinty RJ, Liang X-Z, Dominska M, et al. Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements. PLoS Genet. 2023 Jan;19(1):e1010590.
Qi, Lei, et al. “Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements.PLoS Genet, vol. 19, no. 1, Jan. 2023, p. e1010590. Pubmed, doi:10.1371/journal.pgen.1010590.
Qi L, Sui Y, Tang X-X, McGinty RJ, Liang X-Z, Dominska M, Zhang K, Mirkin SM, Zheng D-Q, Petes TD. Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements. PLoS Genet. 2023 Jan;19(1):e1010590.

Published In

PLoS Genet

DOI

EISSN

1553-7404

Publication Date

January 2023

Volume

19

Issue

1

Start / End Page

e1010590

Location

United States

Related Subject Headings

  • Saccharomyces cerevisiae
  • Retroelements
  • Humans
  • Homologous Recombination
  • Developmental Biology
  • DNA Breaks, Double-Stranded
  • Chromosome Aberrations
  • CRISPR-Cas Systems
  • 3105 Genetics
  • 0604 Genetics