Identification of preferential target sites for human DNA methyltransferases

Nucleic Acids Res. 2011 Jan;39(1):104-18. doi: 10.1093/nar/gkq774. Epub 2010 Sep 13.


DNA methyltransferases (DNMTs) play an important role in establishing and maintaining DNA methylation. Aberrant expression of DNMTs and their isoforms has been found in many types of cancer, and their contribution to aberrant DNA methylation has been proposed. Here, we generated HEK 293T cells stably transfected with each of 13 different DNMTs (DNMT1, two DNMT3A isoforms, nine DNMT3B isoforms and DNMT3L) and assessed the DNA methylation changes induced by each DNMT. We obtained DNA methylation profiles of DNA repetitive elements and 1505 CpG sites from 808 cancer-related genes. We found that DNMTs have specific and overlapping target sites and their DNA methylation target profiles are a reflection of the DNMT domains. By examining H3K4me3 and H3K27me3 modifications in the 808 gene promoter regions using promoter ChIP-on-chip analysis, we found that specific de novo DNA methylation target sites of DNMT3A1 are associated with H3K4me3 modification that are transcriptionally active, whereas the specific target sites of DNMT3B1 are associated with H3K27me3 modification that are transcriptionally inactive. Our data suggest that different DNMT domains are responsible for targeting DNA methylation to specific regions of the genome, and this targeting might be associated with histone modifications.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • CpG Islands
  • DNA (Cytosine-5-)-Methyltransferase 1
  • DNA (Cytosine-5-)-Methyltransferases / chemistry
  • DNA (Cytosine-5-)-Methyltransferases / metabolism*
  • DNA Methylation
  • DNA Methyltransferase 3A
  • Genes, Neoplasm
  • HEK293 Cells
  • Histones / metabolism
  • Humans
  • Isoenzymes / chemistry
  • Isoenzymes / metabolism
  • Protein Structure, Tertiary
  • RNA, Messenger / metabolism
  • Repetitive Sequences, Nucleic Acid


  • DNMT3A protein, human
  • Histones
  • Isoenzymes
  • RNA, Messenger
  • DNMT3L protein, human
  • DNA (Cytosine-5-)-Methyltransferase 1
  • DNA (Cytosine-5-)-Methyltransferases
  • DNA Methyltransferase 3A
  • DNA methyltransferase 3B
  • DNMT1 protein, human