title: Location analysis for the estrogen receptor-alpha reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements.
abstract: Location analysis for estrogen receptor-alpha (ERalpha)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ERalpha-bound loci and quantify the incidence of ERE sequences under two stringencies of detection: <10% and 10-20% nucleotide deviation from the canonical ERE sequence. We demonstrate that approximately 50% of all ERalpha-bound loci do not have a discernable ERE and show that most ERalpha-bound EREs are not perfect consensus EREs. Approximately one-third of all ERalpha-bound ERE sequences reside within repetitive DNA sequences, most commonly of the AluS family. In addition, the 3-bp spacer between the inverted ERE half-sites, rather than being random nucleotides, is C(A/T)G-enriched at bona fide receptor targets. Diverse ERalpha-bound loci were validated using electrophoretic mobility shift assay and ChIP-polymerase chain reaction (PCR). The functional significance of receptor-bound loci was demonstrated using luciferase reporter assays which proved that repetitive element ERE sequences contribute to enhancer function. ChIP-PCR demonstrated estrogen-dependent recruitment of the coactivator SRC3 to these loci in vivo. Our data demonstrate that ERalpha binds to widely variant EREs with less sequence specificity than had previously been suspected and that binding at repetitive and nonrepetitive genomic targets is favored by specific trinucleotide spacers.
authors.affiliation: Department of Human Genetics and the Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Mason
authors.forename: Feng-Jue
authors.initials: FJ
authors.lastname: Shu
authors.forename: Cheng
authors.initials: C
authors.lastname: Wang
authors.forename: Ryan M
authors.initials: RM
authors.lastname: Session
authors.forename: Roland G
authors.initials: RG
authors.lastname: Kallen
authors.forename: Neil
authors.initials: N
authors.lastname: Sidell
authors.forename: Tianwei
authors.initials: T
authors.lastname: Yu
authors.forename: Mei Hui
authors.initials: MH
authors.lastname: Liu
authors.forename: Edwin
authors.initials: E
authors.lastname: Cheung
authors.forename: Caleb B
authors.initials: CB
authors.lastname: Kallen
mesh_terms: D001665:Binding Sites; D045744:Cell Line, Tumor; D004247:DNA / Q000737:chemistry*; D004958:Estradiol / Q000494:pharmacology; D047628:Estrogen Receptor alpha / Q000378:metabolism*; D056426:Genetic Loci; D006801:Humans; D056921:Nuclear Receptor Coactivator 3 / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid; D020218:Response Elements; D014158:Transcription, Genetic
chemical_list: D047628:Estrogen Receptor alpha; D004958:Estradiol; D004247:DNA; D056921:Nuclear Receptor Coactivator 3