title: Whole-genome cartography of estrogen receptor alpha binding sites.
abstract: Using a chromatin immunoprecipitation-paired end diTag cloning and sequencing strategy, we mapped estrogen receptor alpha (ERalpha) binding sites in MCF-7 breast cancer cells. We identified 1,234 high confidence binding clusters of which 94% are projected to be bona fide ERalpha binding regions. Only 5% of the mapped estrogen receptor binding sites are located within 5 kb upstream of the transcriptional start sites of adjacent genes, regions containing the proximal promoters, whereas vast majority of the sites are mapped to intronic or distal locations (>5 kb from 5' and 3' ends of adjacent transcript), suggesting transcriptional regulatory mechanisms over significant physical distances. Of all the identified sites, 71% harbored putative full estrogen response elements (EREs), 25% bore ERE half sites, and only 4% had no recognizable ERE sequences. Genes in the vicinity of ERalpha binding sites were enriched for regulation by estradiol in MCF-7 cells, and their expression profiles in patient samples segregate ERalpha-positive from ERalpha-negative breast tumors. The expression dynamics of the genes adjacent to ERalpha binding sites suggest a direct induction of gene expression through binding to ERE-like sequences, whereas transcriptional repression by ERalpha appears to be through indirect mechanisms. Our analysis also indicates a number of candidate transcription factor binding sites adjacent to occupied EREs at frequencies much greater than by chance, including the previously reported FOXA1 sites, and demonstrate the potential involvement of one such putative adjacent factor, Sp1, in the global regulation of ERalpha target genes. Unexpectedly, we found that only 22%-24% of the bona fide human ERalpha binding sites were overlapping conserved regions in whole genome vertebrate alignments, which suggest limited conservation of functional binding sites. Taken together, this genome-scale analysis suggests complex but definable rules governing ERalpha binding and gene regulation.
authors.affiliation: Genome Institute of Singapore, Singapore, Republic of Singapore.
authors.forename: Chin-Yo
authors.initials: CY
authors.lastname: Lin
authors.forename: Vinsensius B
authors.initials: VB
authors.lastname: Vega
authors.forename: Jane S
authors.initials: JS
authors.lastname: Thomsen
authors.forename: Tao
authors.initials: T
authors.lastname: Zhang
authors.forename: Say Li
authors.initials: SL
authors.lastname: Kong
authors.forename: Min
authors.initials: M
authors.lastname: Xie
authors.forename: Kuo Ping
authors.initials: KP
authors.lastname: Chiu
authors.forename: Leonard
authors.initials: L
authors.lastname: Lipovich
authors.forename: Daniel H
authors.initials: DH
authors.lastname: Barnett
authors.forename: Fabio
authors.initials: F
authors.lastname: Stossi
authors.forename: Ailing
authors.initials: A
authors.lastname: Yeo
authors.forename: Joshy
authors.initials: J
authors.lastname: George
authors.forename: Vladimir A
authors.initials: VA
authors.lastname: Kuznetsov
authors.forename: Yew Kok
authors.initials: YK
authors.lastname: Lee
authors.forename: Tze Howe
authors.initials: TH
authors.lastname: Charn
authors.forename: Nallasivam
authors.initials: N
authors.lastname: Palanisamy
authors.forename: Lance D
authors.initials: LD
authors.lastname: Miller
authors.forename: Edwin
authors.initials: E
authors.lastname: Cheung
authors.forename: Benita S
authors.initials: BS
authors.lastname: Katzenellenbogen
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
authors.forename: Guillaume
authors.initials: G
authors.lastname: Bourque
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
authors.forename: Edison T
authors.initials: ET
authors.lastname: Liu
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000235:genetics; D045744:Cell Line, Tumor; D004247:DNA / Q000378:metabolism*; D047628:Estrogen Receptor alpha / Q000235:genetics / Q000378:metabolism*; D005260:Female; D005786:Gene Expression Regulation / Q000502:physiology; D015894:Genome, Human; D006801:Humans
chemical_list: D047628:Estrogen Receptor alpha; D004247:DNA