Diverse DNA methylation statuses at alternative promoters of human genes in various tissues

Jieun Cheong, Yoichi Yamada, Riu Yamashita, Takuma Irie, Akinori Kanai, Hiroyuki Wakaguri, Kenta Nakai, Takashi Ito, Izumu Saito, Sumio Sugano, Yutaka Suzuki

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Abstract

We characterized the DNA methylation status at 144 tissue-biased and 37 non-tissue-biased alternative promoters of 61 human genes in five normal tissues. Analysis of the collected data revealed that (i) DNA methylation status differed greatly among alternative promoters belonging to the same gene; (ii) DNA methylation status differed between tissues for the majority of the individual promoters, and (iii) 80-90% of CpG-island-containing promoters were not methylated on either allele throughout the five tissues examined. Furthermore, although the statistical significance was not as clear as for the above features, we also found that (iv) the DNA methylation patterns of tissue-biased promoters changed more drastically than those of non-tissue-biased promoters; (v) tissue-biased promoters tended to be less methylated than their respective alternative promoters in the tissues where they were preferentially expressed, and (vi) the 'null' methylation pattern of a given promoter was enriched in the tissues where the transcription was most active. These findings together indicate that there are dynamic physiological changes of DNA methylation. DNA methylation appears to play a significant role in differential usage of alternative promoters and may be related to functional diversification between CpG-island-containing promoters and CpG-island-less promoters.

Original languageEnglish
Pages (from-to)155-167
Number of pages13
JournalDNA Research
Volume13
Issue number4
DOIs
Publication statusPublished - Nov 16 2006
Externally publishedYes

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DNA Methylation
CpG Islands
Genes
Methylation
Alleles

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Cheong, J., Yamada, Y., Yamashita, R., Irie, T., Kanai, A., Wakaguri, H., ... Suzuki, Y. (2006). Diverse DNA methylation statuses at alternative promoters of human genes in various tissues. DNA Research, 13(4), 155-167. https://doi.org/10.1093/dnares/dsl008

Diverse DNA methylation statuses at alternative promoters of human genes in various tissues. / Cheong, Jieun; Yamada, Yoichi; Yamashita, Riu; Irie, Takuma; Kanai, Akinori; Wakaguri, Hiroyuki; Nakai, Kenta; Ito, Takashi; Saito, Izumu; Sugano, Sumio; Suzuki, Yutaka.

In: DNA Research, Vol. 13, No. 4, 16.11.2006, p. 155-167.

Research output: Contribution to journalArticle

Cheong, J, Yamada, Y, Yamashita, R, Irie, T, Kanai, A, Wakaguri, H, Nakai, K, Ito, T, Saito, I, Sugano, S & Suzuki, Y 2006, 'Diverse DNA methylation statuses at alternative promoters of human genes in various tissues', DNA Research, vol. 13, no. 4, pp. 155-167. https://doi.org/10.1093/dnares/dsl008
Cheong J, Yamada Y, Yamashita R, Irie T, Kanai A, Wakaguri H et al. Diverse DNA methylation statuses at alternative promoters of human genes in various tissues. DNA Research. 2006 Nov 16;13(4):155-167. https://doi.org/10.1093/dnares/dsl008
Cheong, Jieun ; Yamada, Yoichi ; Yamashita, Riu ; Irie, Takuma ; Kanai, Akinori ; Wakaguri, Hiroyuki ; Nakai, Kenta ; Ito, Takashi ; Saito, Izumu ; Sugano, Sumio ; Suzuki, Yutaka. / Diverse DNA methylation statuses at alternative promoters of human genes in various tissues. In: DNA Research. 2006 ; Vol. 13, No. 4. pp. 155-167.
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