ArticleGenome biology2011
A genome-wide view of mutation rate co-variation using multivariate analyses.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 38 citations in OpenAlex.
- Effects of parental age and polymer composition on short tandem repeat de novo mutation rates.Genetics · 2024Article
- Genomic diversity landscapes in outcrossing and selfing Caenorhabditis nematodes.PLoS genetics · 2023Article
- Very Low Rates of Spontaneous Gene Deletions and Gene Duplications in Dictyostelium discoideum.Journal of molecular evolution · 2023Article
- Mutational Signatures of Replication Timing and Epigenetic Modification Persist through the Global Divergence of Mutation Spectra across the Great Ape Phylogeny.Genome biology and evolution · 2022Article
- Engines of change: Transposable element mutation rates are high and variable within Daphnia magna.PLoS genetics · 2021Article
- Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome.Nucleic acids research · 2021Article
- Extreme differences between human germline and tumor mutation densities are driven by ancestral human-specific deviations.Nature communications · 2020Article
- Nuclear topology modulates the mutational landscapes of cancer genomes.Nature structural & molecular biology · 2017Article
- Evolution of Local Mutation Rate and Its Determinants.Molecular biology and evolution · 2017Article
- Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats.Molecular biology and evolution · 2016Article
- Variation in the molecular clock of primates.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity.Molecular ecology · 2016Article
- SNP Formation Bias in the Murine Genome Provides Evidence for Parallel Evolution.Genome biology and evolution · 2015Article
- Breaking bad: The mutagenic effect of DNA repair.DNA repair · 2015Review
- Limits and patterns of cytomegalovirus genomic diversity in humans.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- The effects of chromatin organization on variation in mutation rates in the genome.Nature reviews. Genetics · 2015Review
- Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition.Genome research · 2014Article
- DNA methylation is associated with an increased level of conservation at nondegenerate nucleotides in mammals.Molecular biology and evolution · 2014Article
- Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome.Molecular biology and evolution · 2014Article
- Segmenting the human genome based on states of neutral genetic divergence.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
backgroundWhile the abundance of available sequenced genomes has led to many studies of regional heterogeneity in mutation rates, the co-variation among rates of different mutation types remains largely unexplored, hindering a deeper understanding of mutagenesis and genome dynamics. Here, utilizing primate and rodent genomic alignments, we apply two multivariate analysis techniques (principal components and canonical correlations) to investigate the structure of rate co-variation for four mutation types and simultaneously explore the associations with multiple genomic features at different genomic scales and phylogenetic distances.
resultsWe observe a consistent, largely linear co-variation among rates of nucleotide substitutions, small insertions and small deletions, with some non-linear associations detected among these rates on chromosome X and near autosomal telomeres. This co-variation appears to be shaped by a common set of genomic features, some previously investigated and some novel to this study (nuclear lamina binding sites, methylated non-CpG sites and nucleosome-free regions). Strong non-linear relationships are also detected among genomic features near the centromeres of large chromosomes. Microsatellite mutability co-varies with other mutation rates at finer scales, but not at 1 Mb, and shows varying degrees of association with genomic features at different scales.
conclusionsOur results allow us to speculate about the role of different molecular mechanisms, such as replication, recombination, repair and local chromatin environment, in mutagenesis. The software tools developed for our analyses are available through Galaxy, an open-source genomics portal, to facilitate the use of multivariate techniques in future large-scale genomics studies.
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