Development of a novel microRNA promoter microarray for ChIP-on-chip assay to identify epigenetically regulated microRNAs

Yoshimasa Saito, Hidekazu Suzuki, Toshiki Taya, Masafumi Nishizawa, Hitoshi Tsugawa, Juntaro Matsuzaki, Kenro Hirata, Hidetsugu Saito, Toshifumi Hibi

Research output: Contribution to journalArticlepeer-review

17 Citations (Scopus)


To gain a global view of epigenetic alterations around microRNA (miRNA) promoter regions, and to identify epigenetically regulated miRNAs, we developed a novel miRNA promoter microarray for chromatin immunoprecipitation (ChIP)-on-chip assay. We designed a custom oligo microarray covering regions spanning -10 to +2.5. kb of precursor miRNAs in the human genome. This microarray covers 541 miRNAs, each of which is covered by approximately 100 probes (60-mer) over its 12.5-kb genomic position, that includes predicted transcription start sites. Using this custom-made miRNA promoter microarray, we successfully performed ChIP-on-chip assay to identify miRNAs regulated by histone modification. Fifty-three miRNAs (9.8%) showed increased levels of both histone H3 acetylation and histone H3-K4 methylation in AGS gastric cancer cells treated with the DNA-methylation inhibitor 5-aza-2'-deoxycytidine and the histone deacetylase inhibitor 4-phenylbutyric acid. One of these miRNAs, miR-9, is downregulated in gastric cancer tissues and is activated by chromatin-modifying drugs, suggesting that it may be a potential target for epigenetic therapy of gastric cancer.

Original languageEnglish
Pages (from-to)33-37
Number of pages5
JournalBiochemical and Biophysical Research Communications
Issue number1
Publication statusPublished - 2012 Sept 14


  • ChIP-on-chip
  • Epigenetic therapy
  • Epigenetics
  • Gastric cancer
  • Histone modification
  • MiR-9
  • MicroRNA

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology


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