ArticleProceedings of the National Academy of Sciences of the United States of America2016
Repair of adjacent single-strand breaks is often accompanied by the formation of tandem sequence duplications in plant genomes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 73 citations in OpenAlex.
- Article
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- Context effects on repair of 5'-overhang DNA double-strand breaks induced by Cas12a in Arabidopsis.Plant direct · 2024Article
- On- and off-target effects of paired CRISPR-Cas nickase in primary human cells.Molecular therapy : the journal of the American Society of Gene Therapy · 2024Article
- CRISPR/Cas9 mediated genome editing tools and their possible role in disease resistance mechanism.Molecular biology reports · 2022Review
- SIQ: easy quantitative measurement of mutation profiles in sequencing data.NAR genomics and bioinformatics · 2022Article
- Nonhomologous end joining as key to CRISPR/Cas-mediated plant chromosome engineering.Plant physiology · 2022Article
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- Engineering broad-spectrum resistance to cotton leaf curl disease by CRISPR-Cas9 based multiplex editing in plants.GM crops & food · 2021Article
- Different DNA repair pathways are involved in single-strand break-induced genomic changes in plants.The Plant cell · 2021Article
- CRISPR/dCas9-Based Systems: Mechanisms and Applications in Plant Sciences.Plants (Basel, Switzerland) · 2021Review
- Small tandem DNA duplications result from CST-guided Pol α-primase action at DNA break termini.Nature communications · 2021Article
- Novel CRISPR/Cas applications in plants: from prime editing to chromosome engineering.Transgenic research · 2021Review
- Boon and Bane of DNA Double-Strand Breaks.International journal of molecular sciences · 2021Review
- PHACTR1 genetic variability is not critical in small vessel ischemic disease patients and PcomA recruitment in C57BL/6J mice.Scientific reports · 2021Article
- Gene disruption by structural mutations drives selection in US rice breeding over the last century.PLoS genetics · 2021Article
- Microhomologies Are Associated with Tandem Duplications and Structural Variation in Plant Mitochondrial Genomes.Genome biology and evolution · 2020Article
- Applications of CRISPR/Cas to Improve Crop Disease Resistance: Beyond Inactivation of Susceptibility Factors.iScience · 2020Review
- Article
- BRCA1-associated structural variations are a consequence of polymerase theta-mediated end-joining.Nature communications · 2020Article
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3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Duplication of existing sequences is a major mechanism of genome evolution. It has been previously shown that duplications can occur by replication slippage, unequal sister chromatid exchange, homologous recombination, and aberrant double-strand break-induced synthesis-dependent strand annealing reactions. In a recent study, the abundant presence of short direct repeats was documented by comparative bioinformatics analysis of different rice genomes, and the hypothesis was put forward that such duplications might arise due to the concerted repair of adjacent single-strand breaks (SSBs). Applying the CRISPR/Cas9 technology, we were able to test this hypothesis experimentally in the model plant Arabidopsis thaliana Using a Cas9 nickase to induce adjacent genomic SSBs in different regions of the genome (genic, intergenic, and heterochromatic) and at different distances (∼20, 50, and 100 bps), we analyzed the repair outcomes by deep sequencing. In addition to deletions, we regularly detected the formation of direct repeats close to the break sites, independent of the genomic context. The formation of these duplications as well as deletions may be associated with the presence of microhomologies. Most interestingly, we found that even the induction of two SSBs on the same DNA strand can cause genome alterations, albeit at a much lower level. Because such a scenario reflects a natural step during nucleotide excision repair, and given that the germline is set aside only late during development in plants, the repair of adjacent SSBs indeed seems to have an important influence on the shaping of plant genomes during evolution.
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