Cell type-specific methylation profiles occurring disproportionately in CpG-less regions that delineate developmental similarity

Hideki Sakamoto, Masako Suzuki, Tetsuya Abe, Tohru Hosoyama, Emi Himeno, Satoshi Tanaka, John M. Greally, Naka Hattori, Shintaro Yagi, Kunio Shiota

Research output: Contribution to journalArticle

35 Citations (Scopus)

Abstract

Our previous studies using restriction landmark genomic scanning (RLGS) defined tissue- or cell-specific DNA methylation profiles. It remains to be determined whether the DNA sequence compositions in the genomic contexts of the Not I loci tested by RLGS influence their tendency to change with differentiation. We carried out 3834 methylation measurements consisting of 213 Not I loci in the mouse genome in 18 different tissues and cell types, using quantitative real-time PCR based on a V irtual image rlgs database. Loci were categorized as CpG islands or other, and as unique or repetitive sequences, each category being associated with a variety of methylation categories. Strikingly, the tissue-dependently and differentially methylated regions (T-DMRs) were disproportionately distributed in the non-CpG island loci. These loci were located not only in 5′-upstream regions of genes but also in intronic and non-genic regions. Hierarchical clustering of the methylation profiles could be used to define developmental similarity and cellular phenotypes. The results show that distinctive tissue- and cell type-specific methylation profiles by RLGS occur mostly at Not I sites located at non-CpG island sequences, which delineate developmental similarity of different cell types. The finding indicates the power of Not I methylation profiles in evaluating the relatedness of different cell types.

Original languageEnglish
Pages (from-to)1123-1132
Number of pages10
JournalGenes to Cells
Volume12
Issue number10
DOIs
Publication statusPublished - 2007 Oct
Externally publishedYes

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Methylation
Islands
CpG Islands
Nucleic Acid Repetitive Sequences
DNA Methylation
Cluster Analysis
Real-Time Polymerase Chain Reaction
Genome
Databases
Phenotype
Genes

ASJC Scopus subject areas

  • Genetics
  • Cell Biology

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Cell type-specific methylation profiles occurring disproportionately in CpG-less regions that delineate developmental similarity. / Sakamoto, Hideki; Suzuki, Masako; Abe, Tetsuya; Hosoyama, Tohru; Himeno, Emi; Tanaka, Satoshi; Greally, John M.; Hattori, Naka; Yagi, Shintaro; Shiota, Kunio.

In: Genes to Cells, Vol. 12, No. 10, 10.2007, p. 1123-1132.

Research output: Contribution to journalArticle

Sakamoto, H, Suzuki, M, Abe, T, Hosoyama, T, Himeno, E, Tanaka, S, Greally, JM, Hattori, N, Yagi, S & Shiota, K 2007, 'Cell type-specific methylation profiles occurring disproportionately in CpG-less regions that delineate developmental similarity', Genes to Cells, vol. 12, no. 10, pp. 1123-1132. https://doi.org/10.1111/j.1365-2443.2007.01120.x
Sakamoto, Hideki ; Suzuki, Masako ; Abe, Tetsuya ; Hosoyama, Tohru ; Himeno, Emi ; Tanaka, Satoshi ; Greally, John M. ; Hattori, Naka ; Yagi, Shintaro ; Shiota, Kunio. / Cell type-specific methylation profiles occurring disproportionately in CpG-less regions that delineate developmental similarity. In: Genes to Cells. 2007 ; Vol. 12, No. 10. pp. 1123-1132.
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