The genomic loci of specific human tRNA genes exhibit ageing-related DNA hypermethylation

Nat Commun. 2021 May 11;12(1):2655. doi: 10.1038/s41467-021-22639-6.

Abstract

The epigenome has been shown to deteriorate with age, potentially impacting on ageing-related disease. tRNA, while arising from only ˜46 kb (<0.002% genome), is the second most abundant cellular transcript. tRNAs also control metabolic processes known to affect ageing, through core translational and additional regulatory roles. Here, we interrogate the DNA methylation state of the genomic loci of human tRNA. We identify a genomic enrichment for age-related DNA hypermethylation at tRNA loci. Analysis in 4,350 MeDIP-seq peripheral-blood DNA methylomes (16-82 years), identifies 44 and 21 hypermethylating specific tRNAs at study-and genome-wide significance, respectively, contrasting with none hypomethylating. Validation and replication (450k array and independent targeted Bisuphite-sequencing) supported the hypermethylation of this functional unit. Tissue-specificity is a significant driver, although the strongest consistent signals, also independent of major cell-type change, occur in tRNA-iMet-CAT-1-4 and tRNA-Ser-AGA-2-6. This study presents a comprehensive evaluation of the genomic DNA methylation state of human tRNA genes and reveals a discreet hypermethylation with advancing age.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Aged, 80 and over
  • Aging / genetics*
  • Animals
  • Child
  • Child, Preschool
  • CpG Islands / genetics*
  • DNA Methylation*
  • Female
  • Genome, Human / genetics*
  • Humans
  • Male
  • Mice
  • Middle Aged
  • Neoplasms / genetics
  • Neoplasms / pathology
  • Organ Specificity / genetics
  • RNA, Transfer / genetics*
  • Young Adult

Substances

  • RNA, Transfer