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 journalArticle

15 Citations (Scopus)

Abstract

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
Volume426
Issue number1
DOIs
Publication statusPublished - 2012 Sep 14

Fingerprint

Chromatin Immunoprecipitation
Microarrays
MicroRNAs
Chromatin
Assays
Histones
Stomach Neoplasms
decitabine
Epigenomics
Histone Code
Acetylation
Histone Deacetylase Inhibitors
Methylation
Transcription Initiation Site
Human Genome
DNA Methylation
Genetic Promoter Regions
Down-Regulation
Genes
Cells

Keywords

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

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Cell Biology
  • Molecular Biology

Cite this

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abstract = "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.",
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AU - Suzuki, Hidekazu

AU - Taya, Toshiki

AU - Nishizawa, Masafumi

AU - Tsugawa, Hitoshi

AU - Matsuzaki, Juntaro

AU - Hirata, Kenro

AU - Saito, Hidetsugu

AU - Hibi, Toshifumi

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