Redox-active quinones induces genome-wide DNA methylation changes by an iron-mediated and Tet-dependent mechanism

Nucleic Acids Res. 2014 Feb;42(3):1593-605. doi: 10.1093/nar/gkt1090. Epub 2013 Nov 8.

Abstract

DNA methylation has been proven to be a critical epigenetic mark important for various cellular processes. Here, we report that redox-active quinones, a ubiquitous class of chemicals found in natural products, cancer therapeutics and environment, stimulate the conversion of 5 mC to 5 hmC in vivo, and increase 5 hmC in 5751 genes in cells. 5 hmC increase is associated with significantly altered gene expression of 3414 genes. Interestingly, in quinone-treated cells, labile iron-sensitive protein ferritin light chain showed a significant increase at both mRNA and protein levels indicating a role of iron regulation in stimulating Tet-mediated 5 mC oxidation. Consistently, the deprivation of cellular labile iron using specific chelator blocked the 5 hmC increase, and a delivery of labile iron increased the 5 hmC level. Moreover, both Tet1/Tet2 knockout and dimethyloxalylglycine-induced Tet inhibition diminished the 5 hmC increase. These results suggest an iron-regulated Tet-dependent DNA demethylation mechanism mediated by redox-active biomolecules.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5-Methylcytosine / metabolism
  • Animals
  • Apoferritins / biosynthesis
  • Apoferritins / genetics
  • Cell Line
  • Cell Line, Tumor
  • Chloranil / pharmacology
  • Cytosine / analogs & derivatives
  • Cytosine / metabolism
  • DNA Methylation* / drug effects
  • DNA-Binding Proteins / genetics
  • Dioxygenases / metabolism*
  • Gene Expression Regulation
  • Genome
  • Humans
  • Iron / metabolism*
  • Mice
  • Oxidation-Reduction
  • Proto-Oncogene Proteins / genetics
  • Quinones / chemistry
  • Quinones / pharmacology*

Substances

  • DNA-Binding Proteins
  • Proto-Oncogene Proteins
  • Quinones
  • TET1 protein, mouse
  • Chloranil
  • 5-hydroxymethylcytosine
  • 5-Methylcytosine
  • Cytosine
  • Apoferritins
  • Iron
  • Dioxygenases
  • Tet2 protein, mouse

Associated data

  • GEO/GSE44457