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

Ryonosuke Yamaga; Kazuhiro Ikeda; Joost Boele; Kuniko Horie-Inoue; Ken-Ichi Takayama; Tomohiko Urano; Kaoru Kaida; Piero Carninci; Jun Kawai; Yoshihide Hayashizaki; Yasuyoshi Ouchi; Michiel de Hoon; Satoshi Inoue

doi:10.1016/j.bbrc.2014.04.033

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

Biochem Biophys Res Commun. 2014 May 9;447(3):531-6. doi: 10.1016/j.bbrc.2014.04.033. Epub 2014 Apr 16.

Authors

Affiliations

¹ Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan; Department of Geriatric Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
² Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan.
³ Department of Systems Bioinformatics, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, Amsterdam, the Netherlands; RIKEN Omics Science Center, Yokohama, Kanagawa, Japan(1).
⁴ Department of Geriatric Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
⁵ RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa, Japan; RIKEN Omics Science Center, Yokohama, Kanagawa, Japan(1).
⁶ RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama, Japan; RIKEN Omics Science Center, Yokohama, Kanagawa, Japan(1).
⁷ Department of Geriatric Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
⁸ Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Saitama, Japan; Department of Geriatric Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. Electronic address: [email protected].

PMID: 24746470
DOI: 10.1016/j.bbrc.2014.04.033

Abstract

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 (⩽10 kb) 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.

Keywords: Breast cancer; Cap analysis of gene expression; Estrogen; Transcriptome.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Breast Neoplasms / genetics*
Breast Neoplasms / metabolism
Cell Line, Tumor
Chromosome Mapping
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

Substances

Estrogen Receptor alpha
Estrogens