ArticleProceedings of the National Academy of Sciences of the United States of America2012
Position-dependent correlations between DNA methylation and the evolutionary rates of mammalian coding exons.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 48 citations in OpenAlex.
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- Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement.Genome biology · 2024Article
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- Cell-type-specific epigenetic effects of early life stress on the brain.Translational psychiatry · 2022Review
- Koala methylomes reveal divergent and conserved DNA methylation signatures of X chromosome regulation.Proceedings. Biological sciences · 2021Article
- Machine learning analyses of methylation profiles uncovers tissue-specific gene expression patterns in wheat.The plant genome · 2020Article
- Characterization of Global DNA Methylation in Different Gene Regions Reveals Candidate Biomarkers in Pigs with High and Low Levels of Boar Taint.Veterinary sciences · 2020Article
- Whole-genome fingerprint of the DNA methylome during chemically induced differentiation of the human AML cell line HL-60/S4.Biology open · 2020Article
- A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations.Genome research · 2019Article
- Antagonistic and synergistic epigenetic modulation using orthologous CRISPR/dCas9-based modular system.Nucleic acids research · 2019Article
- Identification of DNA motifs that regulate DNA methylation.Nucleic acids research · 2019Article
- NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors.BMC bioinformatics · 2019Article
- The association between DNA methylation and exon expression in the Pacific oyster Crassostrea gigas.PloS one · 2017Article
- Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines.BMC systems biology · 2016Article
- Mapping epigenetic changes to the host cell genome induced by Burkholderia pseudomallei reveals pathogen-specific and pathogen-generic signatures of infection.Scientific reports · 2016Article
- The evolution of the coding exome of the Arabidopsis species--the influences of DNA methylation, relative exon position, and exon length.BMC evolutionary biology · 2014Article
- Impacts of pretranscriptional DNA methylation, transcriptional transcription factor, and posttranscriptional microRNA regulations on protein evolutionary rate.Genome biology and evolution · 2014Article
- DNA methylation and evolution of duplicate genes.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA cytosine methylation is a central epigenetic marker that is usually mutagenic and may increase the level of sequence divergence. However, methylated genes have been reported to evolve more slowly than unmethylated genes. Hence, there is a controversy on whether DNA methylation is correlated with increased or decreased protein evolutionary rates. We hypothesize that this controversy has resulted from the differential correlations between DNA methylation and the evolutionary rates of coding exons in different genic positions. To test this hypothesis, we compare human-mouse and human-macaque exonic evolutionary rates against experimentally determined single-base resolution DNA methylation data derived from multiple human cell types. We show that DNA methylation is significantly related to within-gene variations in evolutionary rates. First, DNA methylation level is more strongly correlated with C-to-T mutations at CpG dinucleotides in the first coding exons than in the internal and last exons, although it is positively correlated with the synonymous substitution rate in all exon positions. Second, for the first exons, DNA methylation level is negatively correlated with exonic expression level, but positively correlated with both nonsynonymous substitution rate and the sample specificity of DNA methylation level. For the internal and last exons, however, we observe the opposite correlations. Our results imply that DNA methylation level is differentially correlated with the biological (and evolutionary) features of coding exons in different genic positions. The first exons appear more prone to the mutagenic effects, whereas the other exons are more influenced by the regulatory effects of DNA methylation.
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