Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation

Curr Biol. 2002 Aug 20;12(16):1360-7. doi: 10.1016/s0960-9822(02)00976-4.


Background: The heterochromatin of many eukaryotes is marked by both DNA methylation and histone H3 lysine 9 (H3-K9) methylation, though the exact relationship between these epigenetic modifications is unknown. In Neurospora, H3-K9 methylation is required for the maintenance of all known DNA methylation. In Arabidopsis, H3-K9 methylation directs some of the CpNpG and asymmetric methylation. However, it is not known in any organism whether DNA methylation may also direct histone H3 methylation.

Results: Using chromatin immunoprecipitation (ChIP) assays, we show that Arabidopsis heterochromatin is associated with H3-K9 methylation. This histone methylation is dependent on the KRYPTONITE and DDM1 genes (SU[VAR]3-9 and SWI2/SNF2 homologs, respectively). We also find that a decrease in DNA methylation does not directly cause a loss of H3-K9 methylation. Instead, a decrease in H3-K9 methylation is only seen at loci where transcription is derepressed.

Conclusions: We conclude that DNA methylation does not control the methylation of histone H3-K9. We propose that loss of H3-K9 methylation is due to transcriptional reactivation, coupled with deposition of unmethylated nucleosomes. These findings are consistent with recent observations of DNA replication-independent deposition of histone H3.3 in Drosophila. Our results also suggest that, in Arabidopsis, DNA methylation is sufficient for gene silencing, but H3-K9 methylation is not.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Arabidopsis Proteins*
  • Chromatin / genetics
  • Chromatin / metabolism
  • DNA (Cytosine-5-)-Methyltransferases / genetics
  • DNA (Cytosine-5-)-Methyltransferases / metabolism
  • DNA Methylation*
  • DNA, Plant / metabolism*
  • DNA-Cytosine Methylases / genetics
  • DNA-Cytosine Methylases / metabolism
  • Gene Silencing
  • Genes, Plant
  • Histones / metabolism*
  • Methylation
  • Precipitin Tests
  • Retroelements / genetics
  • Transcription Factors / genetics


  • Arabidopsis Proteins
  • Chromatin
  • DNA, Plant
  • Histones
  • Retroelements
  • Transcription Factors
  • superman protein, Arabidopsis
  • DNA-Cytosine Methylases
  • MET1 protein, Arabidopsis
  • CMT3 protein, Arabidopsis
  • DNA (Cytosine-5-)-Methyltransferases