ArticleNucleic acids research2015
Differences in genome-wide repeat sequence instability conferred by proofreading and mismatch repair defects.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
30 citing papers in PubMed, 37 citations in OpenAlex.
- Two distinct Okazaki fragment failure modes dominate mutagenesis in the absence of flap endonuclease 1.Nature communications · 2026Article
- Mechanisms underlying low mutation rates in mammalian oocytes and preimplantation embryos.Nucleic acids research · 2025Review
- Evidence that transient replication errors initiate nuclear genome mutations.Nucleic acids research · 2025Article
- A redefined InDel taxonomy provides insights into mutational signatures.Nature genetics · 2025Article
- Mutational signature analysis predicts bacterial hypermutation and multidrug resistance.Nature communications · 2025Article
- Evidence that DNA polymerase δ proofreads errors made by DNA polymerase α across the Saccharomyces cerevisiae nuclear genome.DNA repair · 2024Article
- Genome-Wide Development and Characterization of Microsatellite Markers in the Great Web-Spinning SawflyEcology and evolution · 2024Article
- High fidelity DNA ligation prevents single base insertions in the yeast genome.Nature communications · 2024Article
- Instability throughout the Saccharomyces cerevisiae genome resulting from Pms1 endonuclease deficiency.Nucleic acids research · 2024Article
- The rate of spontaneous mutations in yeast deficient for MutSβ function.G3 (Bethesda, Md.) · 2023Article
- Single-Cell Mononucleotide Microsatellite Analysis Reveals Differential Insertion-Deletion Dynamics in Mouse T Cells.Frontiers in genetics · 2022Article
- Evaluation of repair activity by quantification of ribonucleotides in the genome.Genes to cells : devoted to molecular & cellular mechanisms · 2021Article
- Stability across the Whole Nuclear Genome in the Presence and Absence of DNA Mismatch Repair.Cells · 2021Review
- Thermal stress acceleratesGenome research · 2021Article
- Variable Spontaneous Mutation and Loss of Heterozygosity among Heterozygous Genomes in Yeast.Molecular biology and evolution · 2020Article
- Single-Cell Sequencing of Mouse Thymocytes Reveals Mutational Landscape Shaped by Replication Errors, Mismatch Repair, and H3K36me3.iScience · 2020Article
- Genome-wide mutagenesis resulting from topoisomerase 1-processing of unrepaired ribonucleotides in DNA.DNA repair · 2019Article
- R-loop formation by dCas9 is mutagenic in Saccharomyces cerevisiae.Nucleic acids research · 2019Article
- Coordinated protein and DNA conformational changes govern mismatch repair initiation by MutS.Nucleic acids research · 2018Article
- Evaluation of mechanisms that may generate DNA lesions triggering antigenic variation in African trypanosomes.PLoS pathogens · 2018Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Mutation rates are used to calibrate molecular clocks and to link genetic variants with human disease. However, mutation rates are not uniform across each eukaryotic genome. Rates for insertion/deletion (indel) mutations have been found to vary widely when examined in vitro and at specific loci in vivo. Here, we report the genome-wide rates of formation and repair of indels made during replication of yeast nuclear DNA. Using over 6000 indels accumulated in four mismatch repair (MMR) defective strains, and statistical corrections for false negatives, we find that indel rates increase by 100 000-fold with increasing homonucleotide run length, representing the greatest effect on replication fidelity of any known genomic parameter. Nonetheless, long genomic homopolymer runs are overrepresented relative to random chance, implying positive selection. Proofreading defects in the replicative polymerases selectively increase indel rates in short repetitive tracts, likely reflecting the distance over which Pols δ and ϵ interact with duplex DNA upstream of the polymerase active site. In contrast, MMR defects hugely increase indel mutagenesis in long repetitive sequences. Because repetitive sequences are not uniformly distributed among genomic functional elements, the quantitatively different consequences on genome-wide repeat sequence instability conferred by defects in proofreading and MMR have important biological implications.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.