title: Estrogen-mediated epigenetic repression of the imprinted gene cyclin-dependent kinase inhibitor 1C in breast cancer cells.
abstract: While tumor suppressor genes frequently undergo epigenetic silencing in cancer, how the instructions directing this transcriptional repression are transmitted in cancer cells remain largely unclear. Expression of cyclin-dependent kinase inhibitor 1C (CDKN1C), an imprinted gene on chromosomal band 11 p15.5, is reduced or lost in the majority of breast cancers. Here, we report that CDKN1C is suppressed by estrogen through epigenetic mechanisms involving the chromatin-interacting noncoding RNA KCNQ1OT1 and CCCTC-binding factor (CTCF). Activation of estrogen signaling reduced CDKN1C expression 3-fold (P < 0.001) and established repressive histone modifications at the 5' regulatory region of the locus. These events were concomitant with induction of KCNQ1OT1 expression as well as increased recruitment of CTCF to both the distal KCNQ1OT1 promoter-associated imprinting control region (ICR) and the CDKN1C locus. Transient depletion of CTCF by small interfering RNA increased CDKN1C expression and significantly reduced the estrogen-mediated repression of CDKN1C. Further studies in breast cancer cell lines indicated that the epigenetic silencing of CDKN1C occurs in part as the result of genetic loss of the inactive methylated 11p15.5 ICR allele (R(2) = 0.612, P < 0.001). We also found a novel cis-encoded antisense transcript, CDKN1C-AS, which is induced by estrogen signaling following pharmacologic inhibition of DNA methyltransferase and histone deacetylase activity. Forced expression of CDKN1C-AS was capable of repressing endogenous CDKN1C in vivo. Our findings suggest that in addition to promoter hypermethylation, epigenetic repression of tumor suppressor genes by CTCF and noncoding RNA transcripts could be more common and important than previously understood.
authors.affiliation: Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA.
authors.forename: Benjamin A T
authors.initials: BA
authors.lastname: Rodriguez
authors.forename: Yu-I
authors.initials: YI
authors.lastname: Weng
authors.forename: Ta-Ming
authors.initials: TM
authors.lastname: Liu
authors.forename: Tao
authors.initials: T
authors.lastname: Zuo
authors.forename: Pei-Yin
authors.initials: PY
authors.lastname: Hsu
authors.forename: Ching-Hung
authors.initials: CH
authors.lastname: Lin
authors.forename: Ann-Lii
authors.initials: AL
authors.lastname: Cheng
authors.forename: Hengmi
authors.initials: H
authors.lastname: Cui
authors.forename: Pearlly S
authors.initials: PS
authors.lastname: Yan
authors.forename: Tim H-M
authors.initials: TH
authors.lastname: Huang
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics*; D000076246:CCCTC-Binding Factor; D047369:Chromatin Immunoprecipitation; D050761:Cyclin-Dependent Kinase Inhibitor p57 / Q000235:genetics*; D019175:DNA Methylation; D044127:Epigenesis, Genetic / Q000235:genetics*; D004967:Estrogens / Q000494:pharmacology*; D005260:Female; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D020868:Gene Silencing / Q000187:drug effects*; D018392:Genomic Imprinting; D006801:Humans; D024642:Potassium Channels, Voltage-Gated / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics; D012097:Repressor Proteins / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014407:Tumor Cells, Cultured
chemical_list: D000076246:CCCTC-Binding Factor; C493964:CDKN1C protein, human; C000619697:CTCF protein, human; D050761:Cyclin-Dependent Kinase Inhibitor p57; D004967:Estrogens; C485621:KCNQ1OT1 long non-coding RNA, human; D024642:Potassium Channels, Voltage-Gated; D012333:RNA, Messenger; D022661:RNA, Untranslated; D012097:Repressor Proteins