Systemic identification of estrogen-regulated genes in breast cancer cells through cap analysis of gene expression mapping

• Published in: Biochemical and biophysical research communications Vol. 447; no. 3; pp. 531 - 536
• Main Authors: Yamaga, Ryonosuke, Ikeda, Kazuhiro, Boele, Joost, Horie-Inoue, Kuniko, Takayama, Ken-ichi, Urano, Tomohiko, Kaida, Kaoru, Carninci, Piero, Kawai, Jun, Hayashizaki, Yoshihide, Ouchi, Yasuyoshi, de Hoon, Michiel, Inoue, Satoshi
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 09.05.2014
• Subjects: Breast cancer; Breast Neoplasms - genetics; Breast Neoplasms - metabolism; Cap analysis of gene expression; Cell Line, Tumor; Chromosome Mapping; Estrogen; Estrogen Receptor alpha - metabolism; Estrogens - metabolism; Estrogens - pharmacology; Female; Gene Expression Profiling - methods; Gene Expression Regulation, Neoplastic; Gene Knockdown Techniques - methods; Genetic Testing; Humans; MCF-7 Cells; Transcriptome; Breast cancer; Cap analysis of gene expression; Estrogen; Transcriptome
• ISSN: 0006-291X; 1090-2104
• DOI: 10.1016/j.bbrc.2014.04.033

•Cap analysis of gene expression sequencing is performed in breast cancer MCF-7 cells.•The method identifies 15 CAGE tag clusters close to estrogen receptor binding sites.•RAMP3, ISOC1 and GPRC5C are estrogen-regulated genes with those CAGE tag clusters.•RAMP3, ISOC1 and GPRC5C will regulate growth/migration of MCF-7 cells.•CAGE sequencing is useful for global identification of estrogen-regulated promoters. To explore the estrogen-regulated genes genome-widely in breast cancer, cap analysis of gene expression (CAGE) sequencing was performed in MCF-7 cells under estrogen treatment. Estrogen-regulated expressional changes were found in 1537 CAGE tag clusters (TCs) (⩾1.5 or ⩽0.66-folds). Among them, 15 TCs were situated in the vicinity of (⩽10kb) reported estrogen receptor-binding sites. Knockdown experiments of the 15 TC-associated genes demonstrated that the genes such as RAMP3, ISOC1 and GPRC5C potentially regulate the growth or migration of MCF-7 cells. These results suggest that CAGE sequencing will reveal novel estrogen target genes in breast cancer.