title: Epigenetic repression of RARRES1 is mediated by methylation of a proximal promoter and a loss of CTCF binding.
abstract: BACKGROUND
  The cis-acting promoter element responsible for epigenetic silencing of retinoic acid receptor responder 1 (RARRES1) by methylation is unclear. Likewise, how aberrant methylation interplays effectors and thus affects breast neoplastic features remains largely unknown.
  
  
  RESULTS
  We first compared methylation occurring at the sequences (-664~+420) flanking the RARRES1 promoter in primary breast carcinomas to that in adjacent benign tissues. Surprisingly, tumor cores displayed significantly elevated methylation occurring solely at the upstream region (-664~-86), while the downstream element (-85~+420) proximal to the transcriptional start site (+1) remained largely unchanged. Yet, hypermethylation at the former did not result in appreciable silencing effect. In contrast, the proximal sequence displayed full promoter activity and methylation of which remarkably silenced RARRES1 transcription. This phenomenon was recapitulated in breast cancer cell lines, in which methylation at the proximal region strikingly coincided with downregulation. We also discovered that CTCF occupancy was enriched at the unmethylayed promoter bound with transcription-active histone markings. Furthermore, knocking-down CTCF expression hampered RARRES1 expression, suggesting CTCF positively regulated RARRES1 transcription presumably by binding to unmethylated promoter poised at transcription-ready state. Moreover, RARRES1 restoration not only impeded cell invasion but also promoted death induced by chemotherapeutic agents, denoting its tumor suppressive effect. Its role of attenuating invasion agreed with data generated from clinical specimens revealing that RARRES1 was generally downregulated in metastatic lymph nodes compared to the tumor cores.
  
  
  CONCLUSIONS
  This report delineated silencing of RARRES1 by hypermethylation is occurring at a proximal promoter element and is associated with a loss of binding to CTCF, an activator for RARRES1 expression. We also revealed the tumor suppressive roles exerted by RARRES1 in part by promoting breast epithelial cell death and by impeding cell invasion that is an important property for metastatic spread.
authors.affiliation: Division of Medical Technology, School of Allied Medical Professions, the Ohio State University Medical Center, Columbus, Ohio, United States of America.
authors.forename: Zhengang
authors.initials: Z
authors.lastname: Peng
authors.forename: Rulong
authors.initials: R
authors.lastname: Shen
authors.forename: Ying-Wei
authors.initials: YW
authors.lastname: Li
authors.forename: Kun-Yu
authors.initials: KY
authors.lastname: Teng
authors.forename: Charles L
authors.initials: CL
authors.lastname: Shapiro
authors.forename: Huey-Jen L
authors.initials: HJ
authors.lastname: Lin
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism; D000076246:CCCTC-Binding Factor; D016923:Cell Death / Q000235:genetics; D045744:Cell Line, Tumor; D019175:DNA Methylation; D015536:Down-Regulation; D057890:Epigenomics / Q000379:methods; D004847:Epithelial Cells / Q000378:metabolism; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D020868:Gene Silencing; D016147:Genes, Tumor Suppressor; D006657:Histones / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008198:Lymph Nodes / Q000378:metabolism; D008207:Lymphatic Metastasis; D008565:Membrane Proteins / Q000235:genetics* / Q000378:metabolism*; D009361:Neoplasm Invasiveness; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012097:Repressor Proteins / Q000235:genetics* / Q000378:metabolism*; D014158:Transcription, Genetic; D015533:Transcriptional Activation / Q000235:genetics
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D006657:Histones; D008565:Membrane Proteins; C452562:RARRES1 protein, human; D012097:Repressor Proteins