Epigenetic regulation of X-linked cancer/germline antigen genes by DNMT1 and DNMT3b

Oncogene. 2006 Nov 2;25(52):6975-85. doi: 10.1038/sj.onc.1209678. Epub 2006 May 22.


We examined the function of two key DNA methyltransferase (DNMT) enzymes in epigenetic regulation of X-linked cancer/germline (CG-X) antigen genes in human cancer cells, using MAGE-A1, NY-ESO-1, and XAGE-1 as models. In HCT116 cells, genetic knockout of DNMT1 caused moderate activation of CG-X genes, DNMT3b knockout had a negligible effect, and double knockout of both enzymes caused robust gene induction. Similarly, dual DNMT knockout caused dramatic hypomethylation of the MAGE-A1 and NY-ESO-1 promoters, DNMT1 knockout showed moderate hypomethylation, and DNMT3b knockout elicited only slight methylation changes. In contrast, both single and double knockout cells showed significant hypomethylation of the XAGE-1 promoter. RNA interference (RNAi) targeting of DNMT1 in HCT116 cells validated the results seen using genetic knockout cells; however, RNAi targeting of DNMT1 in a different colorectal cancer cell line revealed a greater independent role for DNMT1 in mediating CG-X gene repression and promoter methylation in other cell types. Notably, the histone H3 modification pattern at CG-X promoters was altered following DNMT knockout. DNMT1 or DNMT3b knockout reduced dimethylated lysine-9 (diMe-H3K9) levels, but did not significantly affect dimethylated lysine-4 (diMe-H3K4) or acetylated lysine-9 (Ac-H3-K9) levels. In contrast, dual DNMT1/3b knockout reduced the level of diMe-H3K9 and dramatically increased the levels of diMe-H3K4 and Ac-H3K9 at CG-X gene loci. In summary, DNMT1 and DNMT3b were found to perform both redundant and independent functions in epigenetic regulation of CG-X antigen genes in human cancer cells.

Publication types

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

MeSH terms

  • Antigens, Neoplasm / genetics*
  • Blotting, Western
  • Cell Line, Tumor
  • DNA (Cytosine-5-)-Methyltransferase 1
  • DNA (Cytosine-5-)-Methyltransferases / genetics
  • DNA (Cytosine-5-)-Methyltransferases / metabolism*
  • DNA Methylation
  • DNA Primers
  • Epigenesis, Genetic*
  • Gene Expression
  • Gene Expression Regulation, Neoplastic / genetics*
  • Genes, X-Linked / genetics*
  • Histones
  • Humans
  • Melanoma-Specific Antigens
  • Membrane Proteins / genetics
  • Neoplasm Proteins / genetics
  • Promoter Regions, Genetic
  • RNA, Small Interfering
  • Reverse Transcriptase Polymerase Chain Reaction
  • Transcriptional Activation


  • Antigens, Neoplasm
  • CTAG1B protein, human
  • DNA Primers
  • Histones
  • Melanoma-Specific Antigens
  • Membrane Proteins
  • Neoplasm Proteins
  • RNA, Small Interfering
  • XAGE1A protein, human
  • DNA (Cytosine-5-)-Methyltransferase 1
  • DNA (Cytosine-5-)-Methyltransferases
  • DNA methyltransferase 3B
  • DNMT1 protein, human