{"title":"Interconnected Codons: Unravelling the Epigenetic Significance of Flanking Sequences in CpG Dyads","authors":"Leo Douglas Creasey, Eran Tauber","doi":"10.1007/s00239-024-10172-1","DOIUrl":null,"url":null,"abstract":"<p>Hypothesizing that CpG codon dyads, formed by consecutive codons containing a cytosine-guanine pair (NNC-GNN), may play a crucial role in gene function, we conducted an extensive analysis to investigate their distribution and conservation within mammalian genes. Our findings reveal that genes characterized by a high density of CpG codon dyads are notably associated with homeobox domains and RNA polymerase II transcription factors. Conversely, genes exhibiting low CpG codon dyad density have links to DNA damage repair and mitosis. Importantly, our study identifies a re-markable increase in expressed genes that harbor CpG during embryonic development, suggesting their potential involvement in gene regulation at these developmental stages. These results under-score the functional significance of CpG codon dyads in DNA methylation and gene expression, fur-ther demonstrating the coevolution of consecutive codons and their contribution to codon usage bias.</p>","PeriodicalId":16366,"journal":{"name":"Journal of Molecular Evolution","volume":null,"pages":null},"PeriodicalIF":2.1000,"publicationDate":"2024-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Molecular Evolution","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s00239-024-10172-1","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Hypothesizing that CpG codon dyads, formed by consecutive codons containing a cytosine-guanine pair (NNC-GNN), may play a crucial role in gene function, we conducted an extensive analysis to investigate their distribution and conservation within mammalian genes. Our findings reveal that genes characterized by a high density of CpG codon dyads are notably associated with homeobox domains and RNA polymerase II transcription factors. Conversely, genes exhibiting low CpG codon dyad density have links to DNA damage repair and mitosis. Importantly, our study identifies a re-markable increase in expressed genes that harbor CpG during embryonic development, suggesting their potential involvement in gene regulation at these developmental stages. These results under-score the functional significance of CpG codon dyads in DNA methylation and gene expression, fur-ther demonstrating the coevolution of consecutive codons and their contribution to codon usage bias.
期刊介绍：
Journal of Molecular Evolution covers experimental, computational, and theoretical work aimed at deciphering features of molecular evolution and the processes bearing on these features, from the initial formation of macromolecular systems through their evolution at the molecular level, the co-evolution of their functions in cellular and organismal systems, and their influence on organismal adaptation, speciation, and ecology. Topics addressed include the evolution of informational macromolecules and their relation to more complex levels of biological organization, including populations and taxa, as well as the molecular basis for the evolution of ecological interactions of species and the use of molecular data to infer fundamental processes in evolutionary ecology. This coverage accommodates such subfields as new genome sequences, comparative structural and functional genomics, population genetics, the molecular evolution of development, the evolution of gene regulation and gene interaction networks, and in vitro evolution of DNA and RNA, molecular evolutionary ecology, and the development of methods and theory that enable molecular evolutionary inference, including but not limited to, phylogenetic methods.
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