DNA methylation and expression patterns of key tissue-specific genes in adult stem cells and stomach tissues

J Korean Med Sci. 2009 Oct;24(5):918-29. doi: 10.3346/jkms.2009.24.5.918. Epub 2009 Sep 23.


CpG-island margins and non-island-CpG sites round the transcription start sites of CpG-island-positive and -negative genes are methylated to various degrees in a tissue-specific manner. These methylation-variable CpG sites were analyzed to delineate a relationship between the methylation and transcription of the tissue-specific genes. The level of tissue-specific transcription was estimated by counting the number of the total transcripts in the SAGE (serial analysis of gene expression) database. The methylation status of 12 CpG-island margins and 21 non-island CpG sites near the key tissue-specific genes was examined in pluripotent stromal cells obtained from fat and bone marrow samples as well as in lineage-committed cells from marrow bulk, stomach, colon, breast, and thyroid samples. Of the 33 CpG sites examined, 10 non-island-CpG sites, but none of the CpG-island margins were undermethylated concurrent with tissue-specific expression of their nearby genes. The net methylation of the 33 CpG sites and the net amount of non-island-CpG gene transcripts were high in stomach tissues and low in stromal cells. The present findings suggest that the methylation of the non-island-CpG sites is inversely associated with the expression of the nearby genes, and the concert effect of transitional-CpG methylation is linearly associated with the stomach-specific genes lacking CpG-islands.

Keywords: CpG Islands; DNA Methylation; Stem Cells; Stomach; Tissue-Specific Gene.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adipose Tissue / cytology
  • Adolescent
  • Adult
  • Adult Stem Cells / cytology
  • Adult Stem Cells / metabolism*
  • Aged
  • CpG Islands / genetics*
  • DNA Methylation*
  • Female
  • Gastric Mucosa / metabolism*
  • Gene Expression Profiling
  • Humans
  • Male
  • Middle Aged
  • Polymerase Chain Reaction
  • Stomach / cytology
  • Stromal Cells / metabolism
  • Transcription Initiation Site
  • Transcription, Genetic