Epigenetic modification of centromeric chromatin: hypomethylation of DNA sequences in the CENH3-associated chromatin in Arabidopsis thaliana and maize

Plant Cell. 2008 Jan;20(1):25-34. doi: 10.1105/tpc.107.057083. Epub 2008 Jan 31.


The centromere in eukaryotes is defined by the presence of a special histone H3 variant, CENH3. Centromeric chromatin consists of blocks of CENH3-containing nucleosomes interspersed with blocks of canonical H3-containing nucleosomes. However, it is not known how CENH3 is precisely deposited in the centromeres. It has been suggested that epigenetic modifications of the centromeric chromatin may play a role in centromere identity. The centromeres of Arabidopsis thaliana are composed of megabase-sized arrays of a 178-bp satellite repeat. Here, we report that the 178-bp repeats associated with the CENH3-containing chromatin (CEN chromatin) are hypomethylated compared with the same repeats located in the flanking pericentromeric regions. A similar hypomethylation of DNA in CEN chromatin was also revealed in maize (Zea mays). Hypomethylation of the DNA in CEN chromatin is correlated with a significantly reduced level of H3K9me2 in Arabidopsis. We demonstrate that the 178-bp repeats from CEN chromatin display a distinct distribution pattern of the CG and CNG sites, which may provide a foundation for the differential methylation of these repeats. Our results suggest that DNA methylation plays an important role in epigenetic demarcation of the CEN chromatin.

Publication types

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

MeSH terms

  • Arabidopsis / cytology
  • Arabidopsis / genetics*
  • Base Pairing
  • Base Sequence
  • Centromere / metabolism*
  • Chromatin / metabolism*
  • DNA Methylation*
  • DNA, Plant / metabolism
  • Epigenesis, Genetic*
  • Heterochromatin / metabolism
  • Histones / metabolism*
  • Interphase
  • Meiosis
  • Molecular Sequence Data
  • Repetitive Sequences, Nucleic Acid / genetics
  • Zea mays / genetics*


  • Chromatin
  • DNA, Plant
  • Heterochromatin
  • Histones

Associated data

  • GENBANK/EU359480
  • GENBANK/EU359566