Development of a novel microRNA promoter microarray for ChIP-on-chip assay to identify epigenetically regulated microRNAs.
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.
Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Tokyo 160-8582, Japan.
Yoshimasa
Y
Saito
Hidekazu
H
Suzuki
Toshiki
T
Taya
Masafumi
M
Nishizawa
Hitoshi
H
Tsugawa
Juntaro
J
Matsuzaki
Kenro
K
Hirata
Hidetsugu
H
Saito
Toshifumi
T
Hibi
D001374:Azacitidine / Q000031:analogs & derivatives / Q000494:pharmacology; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D015254:DNA Modification Methylases / Q000037:antagonists & inhibitors; D000077209:Decitabine; D015536:Down-Regulation; D044127:Epigenesis, Genetic; D006657:Histones / Q000378:metabolism; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011401:Promoter Regions, Genetic; D013274:Stomach Neoplasms / Q000235:genetics / Q000628:therapy
D006657:Histones; D035683:MicroRNAs; D000077209:Decitabine; D015254:DNA Modification Methylases; D001374:Azacitidine