![]() Ty elements are depicted with black arrows, and centromeres are shown as white ovals or circles. Ectopic recombination between Ty elements resulting in chromosome rearrangements. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist.įig 1. The raw sequencing data are available at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject PRJNA544995.įunding: This study was supported by a National Key Research and Development Program of China Grant (2021YFC2103200) to DQZ, National Natural Science Foundation of China grants (3217002004 to DQZ and 32270086 to KZ), Fundamental Research Funds for the Central Universities (2021XZZX018) to DQZ, MIRA grants from NIH (R35GM118020 to TDP and R35GM130322 to SMM). This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: The raw data of SNP microarray is deposited as a GEO dataset with the accession number GSE205199. Received: JAccepted: DecemPublished: January 26, 2023Ĭopyright: © 2023 Qi et al. PLoS Genet 19(1):Įditor: Gilles Fischer, Sorbonne Universite UFR de Chimie, FRANCE (2023) Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements. Our results provided novel insights into the mechanism of genome evolution as regulated by repetitive sequences.Ĭitation: Qi L, Sui Y, Tang X-X, McGinty RJ, Liang X-Z, Dominska M, et al. In contrast, we also observed a stimulation of allelic mitotic recombination events between homologs, most of which did not involve direct Ty-Ty interactions. DNA sequencing, using both conventional short “reads” and ultra-long “reads”, showed that almost all of these rearrangements had Ty1 elements at their breakpoints. Chromosome rearrangements were stimulated more than 1000-fold. In this report, we present a comprehensive analysis of recombination events induced in both haploid and diploid strains of Saccharomyces cerevisiae by targeting the Ty1 family of retrotransposons with CRISPR/Cas9. Thus, recombination between transposable elements is an important cause of genetic variation. Recombination between elements located on the same chromosome can produce deletions, duplications, and inversions, whereas recombination between transposable elements on non-homologous chromosomes can generate translocations. Transposable elements can affect gene expression and gene function. Our findings demonstrate the importance of DNA lesions in retrotransposons in driving genome evolution. ![]() Finally, we found that haploid and diploid strain have different preferences for the pathways used to repair double-stranded DNA breaks. 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. In contrast, a large proportion (about three-fourths) of the allelic mitotic recombination events have breakpoints in unique sequences. ![]() 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. Using Southern analysis coupled with short- and long-read DNA sequencing, we revealed important features of recombination induced in retrotransposons. In addition, we found elevated rates of mitotic recombination, resulting in loss of heterozygosity. Following Cas9 induction, we observed a significant elevation of chromosome rearrangements such as deletions, duplications and translocations. Here, we explored how Cas9-induced double-strand breaks (DSBs) directed to Ty1 elements produce genomic alterations in this yeast species. In the genome of the yeast Saccharomyces cerevisiae, the most common class of transposon is the retrotransposon Ty1. 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.
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