scholarly journals Influence of Electron–Holes on DNA Sequence-Specific Mutation Rates

2018 ◽  
Vol 10 (4) ◽  
pp. 1039-1047 ◽  
Author(s):  
Martha Y Suárez-Villagrán ◽  
Ricardo B R Azevedo ◽  
John H Miller
Keyword(s):  
Dna Sequence ◽  
Mutation Rates ◽  
Specific Mutation ◽  
Electron Holes

Sex-Specific Mutation Rates in Salmonid Fish

2003 ◽  
Vol 56 (4) ◽  
pp. 458-463 ◽  
Author(s):  
Hans Ellegren ◽  
Anna-Karin Fridolfsson
Keyword(s):  
Salmonid Fish ◽  
Mutation Rates ◽  
Specific Mutation

DNA Sequence Analysis of Spontaneous Mutagenesis in Saccharomyces cerevisiae

Genetics ◽  
1998 ◽  
Vol 148 (4) ◽  
pp. 1491-1505 ◽  
Author(s):  
Bernard A Kunz ◽  
Karthikeyan Ramachandran ◽  
Edward J Vonarx
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Sequence Analysis ◽  
Dna Sequencing ◽  
Dna Sequence ◽  
Budding Yeast ◽  
Spontaneous Mutation ◽  
Dna Sequence Analysis ◽  
Mutation Rates ◽  
Yeast Saccharomyces Cerevisiae ◽  
Spontaneous Mutagenesis

AbstractTo help elucidate the mechanisms involved in spontaneous mutagenesis, DNA sequencing has been applied to characterize the types of mutation whose rates are increased or decreased in mutator or antimutator strains, respectively. Increased spontaneous mutation rates point to malfunctions in genes that normally act to reduce spontaneous mutation, whereas decreased rates are associated with defects in genes whose products are necessary for spontaneous mutagenesis. In this article, we survey and discuss the mutational specificities conferred by mutator and antimutator genes in the budding yeast Saccharomyces cerevisiae. The implications of selected aspects of the data are considered with respect to the mechanisms of spontaneous mutagenesis.

Estimation of the species-specific mutation rates at the DRB1 locus in humans and chimpanzee

2006 ◽  
Vol 68 (5) ◽  
pp. 427-431 ◽  
Author(s):  
J. Ohashi ◽  
I. Naka ◽  
A. Toyoda ◽  
M. Takasu ◽  
K. Tokunaga ◽  
...  
Keyword(s):  
Mutation Rates ◽  
Specific Mutation ◽  
Drb1 Locus ◽  
Species Specific

scholarly journals Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population

2015 ◽  
Author(s):  
Benjamin D Redelings ◽  
Seiji Kumagai ◽  
Liuyang Wang ◽  
Andrey Tatarenkov ◽  
Ann K. Sakai ◽  
...  
Keyword(s):  
Mating System ◽  
Dirichlet Process ◽  
Mutation Rates ◽  
Common Mutation ◽  
Dirichlet Process Prior ◽  
Coalescence Model ◽  
Specific Mutation ◽  
Sampling Formula ◽  
Self Fertilization ◽  
Infinite Alleles Model

We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about pure hermaphroditism, androdioecy, and gynodioecy. We extend the standard coalescence model to accommodate these mating systems, accounting explicitly for multilocus identity disequilibrium, inbreeding depression, and variation in fertility among mating types. We incorporate the Ewens Sampling Formula (ESF) under the infinite-alleles model of mutation to obtain a novel expression for the likelihood of mating system parameters. Our Markov chain Monte Carlo (MCMC) algorithm assigns locus-specific mutation rates, drawn from a common mutation rate distribution that is itself estimated from the data using a Dirichlet Process Prior model. Among the parameters jointly inferred are the population-wide rate of self-fertilization, locus-specific mutation rates, and the number of generations since the most recent outcrossing event for each sampled individual.

scholarly journals DNA Variation in a 5-Mb Region of the X Chromosome and Estimates of Sex-Specific/Type-Specific Mutation Rates

1999 ◽  
Vol 64 (2) ◽  
pp. 508-517 ◽  
Author(s):  
Theodore Anagnostopoulos ◽  
Peter M. Green ◽  
Gabriella Rowley ◽  
Cathryn M. Lewis ◽  
Francesco Giannelli
Keyword(s):  
X Chromosome ◽  
Mutation Rates ◽  
Dna Variation ◽  
Specific Mutation

scholarly journals Maximum-Likelihood Estimation of Site-Specific Mutation Rates in Human Mitochondrial DNA From Partial Phylogenetic Classification

Genetics ◽  
2008 ◽  
Vol 180 (3) ◽  
pp. 1511-1524 ◽  
Author(s):  
Saharon Rosset ◽  
R. Spencer Wells ◽  
David F. Soria-Hernanz ◽  
Chris Tyler-Smith ◽  
Ajay K. Royyuru ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Maximum Likelihood ◽  
Maximum Likelihood Estimation ◽  
Likelihood Estimation ◽  
Mutation Rates ◽  
Site Specific ◽  
Human Mitochondrial Dna ◽  
Specific Mutation ◽  
Phylogenetic Classification

scholarly journals Widespread transcriptional scanning in the testis modulates gene evolution rates

2018 ◽  
Author(s):  
Bo Xia ◽  
Yun Yan ◽  
Maayan Baron ◽  
Florian Wagner ◽  
Dalia Barkley ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Gene Evolution ◽  
Immune Defense ◽  
Mutation Rates ◽  
Evolutionary Time ◽  
Male Germline ◽  
Specific Subset ◽  
Low Diversity ◽  
Human And Mouse ◽  
Fast Evolution

The testis expresses the largest number of genes of any mammalian organ, a finding that has long puzzled molecular biologists. Analyzing our single-cell transcriptomic maps of human and mouse spermatogenesis, we provide evidence that this widespread transcription serves to maintain DNA sequence integrity in the male germline by correcting DNA damage through 'transcriptional scanning'. Supporting this model, we find that genes expressed during spermatogenesis display lower mutation rates on the transcribed strand and have low diversity in the population. Moreover, this effect is fine-tuned by the level of gene expression during spermatogenesis. The unexpressed genes, which in our model do not benefit from transcriptional scanning, diverge faster over evolutionary time-scales and are enriched for sensory and immune-defense functions. Collectively, we propose that transcriptional scanning modulates germline mutation rates in a gene-specific manner, maintaining DNA sequence integrity for the bulk of genes but allowing for fast evolution in a specific subset.

Estimation of DNA Sequence Context-dependent Mutation Rates Using Primate Genomic Sequences

2007 ◽  
Vol 65 (3) ◽  
pp. 207-214 ◽  
Author(s):  
Wei Zhang ◽  
Gerard G. Bouffard ◽  
Susan S. Wallace ◽  
Jeffrey P. Bond ◽  
Keyword(s):  
Dna Sequence ◽  
Genomic Sequences ◽  
Mutation Rates ◽  
Sequence Context ◽  
Context Dependent
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