The evolution of CpG density and lifespan in conserved primate and mammalian promoters

Adam T. McLain, Christopher Faulk

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

Gene promoters are evolutionarily conserved across holozoans and enriched in CpG sites, the target for DNA methylation. As animals age, the epigenetic pattern of DNA methylation degrades, with highly methylated CpG sites gradually becoming demethylated while CpG islands increase in methylation. Across vertebrates, aging is a trait that varies among species. We used this variation to determine whether promoter CpG density correlates with species' maximum lifespan. Human promoter sequences were used to identify conserved regions in 131 mammals and a subset of 28 primate genomes. We identified approximately 1000 gene promoters (5% of the total), that significantly correlated CpG density with lifespan. The correlations were performed via the phylogenetic least squares method to account for trait similarity by common descent using phylogenetic branch lengths. Gene set enrichment analysis revealed no significantly enriched pathways or processes, consistent with the hypothesis that aging is not under positive selection. However, within both mammals and primates, 95% of the promoters showed a positive correlation between increasing CpG density and species lifespan, and two thirds were shared between the primate subset and mammalian datasets. Thus, these genes may require greater buffering capacity against age-related dysregulation of DNA methylation in longer-lived species.

Original languageEnglish (US)
Pages (from-to)561-572
Number of pages12
JournalAging
Volume10
Issue number4
DOIs
StatePublished - Apr 1 2018

Bibliographical note

Funding Information:
We are grateful to Melissa Drown for carefully revising the manuscript. This work was supported by NIH (NIEHS) grant K99 ES022221 (CF), and University of Michigan NIH (NIEHS) grant R01 ES026877 (PI: Dana Dolinoy), as well as the SUNY Polytechnic Institute Research Foundation. The authors have no conflicts of interest and declare no competing financial interests.

Keywords

  • CpG density
  • CpG site
  • DNA methylation
  • Evolution
  • Lifespan
  • Varmints

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