Mutation hot spots in yeast caused by long-range clustering of homopolymeric sequences.
TLDR
This work uses high-coverage whole-genome sequencing of a conditional mismatch repair mutant line of diploid yeast to identify mutations that accumulated after 160 generations of growth and suggests that specific mutation hot spots can contribute disproportionately to the genetic variation that is introduced into populations.About:
This article is published in Cell Reports.The article was published on 2012-01-26 and is currently open access. It has received 35 citations till now. The article focuses on the topics: Mutation (genetic algorithm) & INDEL Mutation.read more
Citations
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Journal ArticleDOI
Eukaryotic Mismatch Repair in Relation to DNA Replication
Thomas A. Kunkel,Dorothy A. Erie +1 more
TL;DR: This review focuses on MMR in light of increasing knowledge about nuclear DNA replication enzymology and the rate and specificity with which mismatches are generated during leading- and lagging-strand replication.
Journal ArticleDOI
Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition
Scott A. Lujan,Anders R. Clausen,Alan B. Clark,Heather K. MacAlpine,David M. MacAlpine,Ewa P. Malc,Piotr A. Mieczkowski,Adam B. Burkholder,David C. Fargo,Dmitry A. Gordenin,Thomas A. Kunkel +10 more
TL;DR: Mutation patterns implicate replication infidelity as one driver of variation in somatic and germline evolution, suggest mechanisms of mutual modulation of genome stability and composition, and predict future observations in specific cancers.
Journal ArticleDOI
Mutation Rates, Spectra, and Genome-Wide Distribution of Spontaneous Mutations in Mismatch Repair Deficient Yeast
TL;DR: A closer scrutiny of tumor suppressors with homopolymeric runs with proximal repeats as the potential drivers of oncogenesis in mismatch repair defective cells is suggested.
Journal ArticleDOI
Genome duplication and mutations in ACE2 cause multicellular, fast-sedimenting phenotypes in evolved Saccharomyces cerevisiae
Bart Oud,Víctor Guadalupe-Medina,Jurgen F. Nijkamp,Dick de Ridder,Jack T. Pronk,Antonius J. A. van Maris,Jean-Marc Daran +6 more
TL;DR: It is shown that whole-genome duplication and a frameshift mutation in ACE2 are sufficient to generate a fast-sedimenting, multicellular phenotype in S. cerevisiae.
Journal ArticleDOI
Two mechanisms produce mutation hotspots at DNA breaks in Escherichia coli.
TL;DR: It is reported that DNA double-strand breaks (DSBs) provoke mutation hotspots via stress-induced mutation in Escherichia coli, indicating that specific genomic regions could be targeted for mutagenesis, and could also promote concerted evolution within genes/gene clusters, an important issue in the evolution of protein functions.
References
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Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino,Ewan Birney +1 more
TL;DR: Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies and is in close agreement with simulated results without read-pair information.
Posted Content
Multivariate and Propensity Score Matching Software with Automated Balance Optimization: The Matching Package for R
TL;DR: RMatching is an R package which provides functions for multivariate and propensity score matching and for finding optimal covariate balance based on a genetic search algorithm.
Journal ArticleDOI
DNA mismatch repair
Thomas A. Kunkel,Dorothy A. Erie +1 more
TL;DR: This review focuses on the biochemical mechanism of MMR replication errors, on structure-function studies of MMR proteins, on how mismatches are recognized, on the process by which the newly replicated strand is identified, and on excision of the replication error.
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Frameshift mutations and the genetic code. This paper is dedicated to Professor Theodosius Dobzhansky on the occasion of his 66th birthday.
George Streisinger,Yoshimi Okada,Joyce Emrich,Judith Newton,Akira Tsugita,Eric Terzaghi,Masayori Inouye +6 more
Journal ArticleDOI
Multivariate and Propensity Score Matching Software with Automated Balance Optimization: The Matching package for R
TL;DR: Matching as mentioned in this paper is an R package which provides functions for multivariate and propensity score matching and for finding optimal covariate balance based on a genetic search algorithm and a variety of univariate and multivariate metrics to determine if balance actually has been obtained.