J Korean Med Sci.  2009 Oct;24(5):918-929. 10.3346/jkms.2009.24.5.918.

DNA Methylation and Expression Patterns of Key Tissue-specific Genes in Adult Stem Cells and Stomach Tissues

• Hong SJ
• Kang MI
• Oh JH
• Jung YC
• Kim YH
• Kim SJ
• Choi SH
• Seo EJ
• Choi SW
• Rhyu MG

• KMID: 1782016
• DOI: http://doi.org/10.3346/jkms.2009.24.5.918

Abstract

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.

Keyword

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

MeSH Terms

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

Figure

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  Fig. 1 A schematic diagram of the methylation-variable CpG sites in transitional-CpG sites close to transcriptional start sites (TSS). The transitional-CpG sites are distinguished from so-called T-DMRs (tissue-dependent differentially methylated regions) widespread in the human genome regardless of gene-control regions.

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  Fig. 2 Schematic diagram of methylation-variable sites and retroelements in the 5'-end regions of the 33 genes examined. Methylation-variable CpG sites were confirmed to be related to the expressed transcript tags in the case of alternative splicing variants.

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  Fig. 3 Standard curves (A) and common PCR DNA sequencing (B) at methylation-variable sites nearest to the TFF1, CDKN2A, and RUNX3 genes. (A) The cycle threshold (Ct) is calculated with relative fluorescence unit (RFU). (B) The box indicates the MSP primer position.

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  Fig. 4 Autoradiograph and ethidium bromide staining of electrophoretic bands of 33 methylation-variable sites examined in stomach tissue. The level of methylation is indicated below each pair of unmethylation (U) and methylation (M) PCR bands.

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  Fig. 5 Methylation profiles of the 33 MSP sites in the fat and bone marrow stromal cells as well as bone marrow bulk, thyroid, breast, colon, and stomach antrum and body samples. Single and double asterisks indicate under- and over-methylation respectively.

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  Fig. 6 Analysis of methylation variable sites examined in adult stromal cells and lineage-committed tissues.

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  Fig. 7 The proportion of CpG-island and non-island-CpG gene transcripts in stem cells and lineage-committed tissues.

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  Fig. 8 A schematic diagram of variable methylation created during asymmetric stem cell division. A progeny cell that attains a low or high level of variable methylation via asymmetric cell division remains a stem-line cell or activates the CpG-poor tissue-specific genes, respectively.

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