Whole-genome cartography of estrogen receptor alpha binding sites.
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.
Lin
Chin-Yo
CY
Genome Institute of Singapore, Singapore, Republic of Singapore.
Vega
Vinsensius B
VB
Thomsen
Jane S
JS
Zhang
Tao
T
Kong
Say Li
SL
Xie
Min
M
Chiu
Kuo Ping
KP
Lipovich
Leonard
L
Barnett
Daniel H
DH
Stossi
Fabio
F
Yeo
Ailing
A
George
Joshy
J
Kuznetsov
Vladimir A
VA
Lee
Yew Kok
YK
Charn
Tze Howe
TH
Palanisamy
Nallasivam
N
Miller
Lance D
LD
Cheung
Edwin
E
Katzenellenbogen
Benita S
BS
Ruan
Yijun
Y
Bourque
Guillaume
G
Wei
Chia-Lin
CL
Liu
Edison T
ET
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
D047628:Estrogen Receptor alpha; D004247:DNA