Evidence for divergence of DNA methylation maintenance and a conserved inhibitory mechanism from DNA demethylation in chickens and mammals

Genes Genomics. 2021 Mar;43(3):269-280. doi: 10.1007/s13258-021-01046-7. Epub 2021 Feb 8.

Abstract

Background: DNA methylation is a significant epigenetic modification that is evolutionarily conserved in various species and often serves as a repressive mark for transcription. DNA methylation levels and patterns are regulated by a balance of opposing enzyme functions, DNA methyltransferases, DNMT1/3A/3B and methylcytosine dioxygenases, TET1/2/3. In mice, the TET enzyme converts DNA cytosine methylation (5mC) to 5-hydroxymethylcytosine (5hmC) at the beginning of fertilisation and gastrulation and initiates a global loss of 5mC, while the 5mC level is increased on the onset of cell differentiation during early embryonic development.

Objective: Global loss and gain of DNA methylation may be differently regulated in diverged species.

Methods: Chicken B-cell lymphoma DT40 cells were used as an avian model to compare differences in the overall regulation of DNA modification with mammals.

Results: We found that DNA methylation is maintained at high levels in DT40 cells through compact chromatin formation, which inhibits TET-mediated demethylation. Human and mouse chromosomes introduced into DT40 cells by cell fusion lost the majority of 5mC, except for human subtelomeric repeats.

Conclusion: Our attempt to elucidate the differences in the epigenetic regulatory mechanisms between birds and mammals explored the evidence that they share a common chromatin-based regulation of TET-DNA access, while chicken DNMT1 is involved in different target sequence recognition systems, suggesting that factors inducing DNMT-DNA association have already diverged.

Keywords: Chicken; DNA methylation; Divergence; Mammalian chromosome.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line, Tumor
  • Cells, Cultured
  • Chickens / genetics
  • Chromatin
  • DNA Demethylation*
  • DNA Methylation*
  • DNA Modification Methylases / metabolism
  • Dioxygenases / metabolism
  • Female
  • Humans
  • Induced Pluripotent Stem Cells / metabolism
  • Mice
  • Mouse Embryonic Stem Cells / metabolism

Substances

  • Chromatin
  • Dioxygenases
  • DNA Modification Methylases