ArticleGenome research2010
The mutational spectrum of non-CpG DNA varies with CpG content.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
34 citing papers in PubMed.
- Effect of methylation on genome mutability in cattle.Genetics, selection, evolution : GSE · 2026Article
- High Nucleotide Diversity Accompanies Differential DNA Methylation in Naturally Diverging Populations.Molecular biology and evolution · 2023Article
- Review
- The Epigenetics of Psychosis: A Structured Review with Representative Loci.Biomedicines · 2022Review
- Epigenetic variation in animal populations: Sources, extent, phenotypic implications, and ecological and evolutionary relevance.Journal of biosciences · 2021Review
- Cryptic genetic variation enhances primate L1 retrotransposon survival by enlarging the functional coiled coil sequence space of ORF1p.PLoS genetics · 2020Article
- Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons.Mobile DNA · 2020Article
- Accurate ethnicity prediction from placental DNA methylation data.Epigenetics & chromatin · 2019Article
- Proteogenomic Analysis of Protein Sequence Alterations in Breast Cancer Cells.Scientific reports · 2019Article
- Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification.Epigenetics · 2019Article
- Discovery of Lineage-Specific Genome Change in Rice Through Analysis of Resequencing Data.Genetics · 2018Article
- Supporting precision medicine by data mining across multi-disciplines: an integrative approach for generating comprehensive linkages between single nucleotide variants (SNVs) and drug-binding sites.Bioinformatics (Oxford, England) · 2017Article
- Facilitation of environmental adaptation and evolution by epigenetic phenotype variation: insights from clonal, invasive, polyploid, and domesticated animals.Environmental epigenetics · 2017Review
- Family History of Early Infant Death Correlates with Earlier Age at Diagnosis But Not Shorter Time to Diagnosis for Severe Combined Immunodeficiency.Frontiers in immunology · 2017Article
- The discovery of LRRK2 p.R1441S, a novel mutation for Parkinson's disease, adds to the complexity of a mutational hotspot.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2016Article
- An expanded sequence context model broadly explains variability in polymorphism levels across the human genome.Nature genetics · 2016Article
- Genes with monoallelic expression contribute disproportionately to genetic diversity in humans.Nature genetics · 2016Article
- The de novo genome assembly and annotation of a female domestic dromedary of North African origin.Molecular ecology resources · 2016Article
- Breaking bad: The mutagenic effect of DNA repair.DNA repair · 2015Review
- Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus.BMC genomics · 2015Article
Corrections and comments
- Commented on by
Authors and funding
2 authors.
Funding
Abstract
The accumulation of base substitutions (mutations) not subject to natural selection is the neutral mutation rate. Because this rate reflects the in vivo processes involved in maintaining the integrity of genetic information, the factors that affect the neutral mutation rate are of considerable interest. Mammals exhibit two dramatically different neutral mutation rates: the CpG mutation rate, wherein the C of most CpGs (i.e., methyl-CpG) mutate at 10-50 times that of C in any other context or of any other base. The latter mutations constitute the non-CpG rate. The high CpG rate results from the spontaneous deamination of methyl-C to T and incomplete restoration of the ensuing T:G mismatches to C:Gs. Here, we determined the neutral non-CpG mutation rate as a function of CpG content by comparing sequence divergence of thousands of pairs of neutrally evolving chimpanzee and human orthologs that differ primarily in CpG content. Both the mutation rate and the mutational spectrum (transition/transversion ratio) of non-CpG residues change in parallel as sigmoidal (logistic) functions of CpG content. As different mechanisms generate transitions and transversions, these results indicate that both mutation rate and mutational processes are contingent on the local CpG content. We consider several possible mechanisms that might explain how CpG exerts these effects.
Indexed as
Identifiers
What OpenQuestion holds
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.