Cargando…

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

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Qi, Lei, Sui, Yang, Tang, Xing-Xing, McGinty, Ryan J., Liang, Xiao-Zhuan, Dominska, Margaret, Zhang, Ke, Mirkin, Sergei M., Zheng, Dao-Qiong, Petes, Thomas D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9879454/
https://www.ncbi.nlm.nih.gov/pubmed/36701275
http://dx.doi.org/10.1371/journal.pgen.1010590
_version_ 1784878692490543104
author Qi, Lei
Sui, Yang
Tang, Xing-Xing
McGinty, Ryan J.
Liang, Xiao-Zhuan
Dominska, Margaret
Zhang, Ke
Mirkin, Sergei M.
Zheng, Dao-Qiong
Petes, Thomas D.
author_facet Qi, Lei
Sui, Yang
Tang, Xing-Xing
McGinty, Ryan J.
Liang, Xiao-Zhuan
Dominska, Margaret
Zhang, Ke
Mirkin, Sergei M.
Zheng, Dao-Qiong
Petes, Thomas D.
author_sort Qi, Lei
collection PubMed
description 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.
format Online
Article
Text
id pubmed-9879454
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-98794542023-01-27 Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements Qi, Lei Sui, Yang Tang, Xing-Xing McGinty, Ryan J. Liang, Xiao-Zhuan Dominska, Margaret Zhang, Ke Mirkin, Sergei M. Zheng, Dao-Qiong Petes, Thomas D. PLoS Genet Research Article 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. Public Library of Science 2023-01-26 /pmc/articles/PMC9879454/ /pubmed/36701275 http://dx.doi.org/10.1371/journal.pgen.1010590 Text en © 2023 Qi et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Qi, Lei
Sui, Yang
Tang, Xing-Xing
McGinty, Ryan J.
Liang, Xiao-Zhuan
Dominska, Margaret
Zhang, Ke
Mirkin, Sergei M.
Zheng, Dao-Qiong
Petes, Thomas D.
Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements
title Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements
title_full Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements
title_fullStr Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements
title_full_unstemmed Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements
title_short Shuffling the yeast genome using CRISPR/Cas9-generated DSBs that target the transposable Ty1 elements
title_sort shuffling the yeast genome using crispr/cas9-generated dsbs that target the transposable ty1 elements
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9879454/
https://www.ncbi.nlm.nih.gov/pubmed/36701275
http://dx.doi.org/10.1371/journal.pgen.1010590
work_keys_str_mv AT qilei shufflingtheyeastgenomeusingcrisprcas9generateddsbsthattargetthetransposablety1elements
AT suiyang shufflingtheyeastgenomeusingcrisprcas9generateddsbsthattargetthetransposablety1elements
AT tangxingxing shufflingtheyeastgenomeusingcrisprcas9generateddsbsthattargetthetransposablety1elements
AT mcgintyryanj shufflingtheyeastgenomeusingcrisprcas9generateddsbsthattargetthetransposablety1elements
AT liangxiaozhuan shufflingtheyeastgenomeusingcrisprcas9generateddsbsthattargetthetransposablety1elements
AT dominskamargaret shufflingtheyeastgenomeusingcrisprcas9generateddsbsthattargetthetransposablety1elements
AT zhangke shufflingtheyeastgenomeusingcrisprcas9generateddsbsthattargetthetransposablety1elements
AT mirkinsergeim shufflingtheyeastgenomeusingcrisprcas9generateddsbsthattargetthetransposablety1elements
AT zhengdaoqiong shufflingtheyeastgenomeusingcrisprcas9generateddsbsthattargetthetransposablety1elements
AT petesthomasd shufflingtheyeastgenomeusingcrisprcas9generateddsbsthattargetthetransposablety1elements