Relationship between estrogen receptor α location and gene induction reveals the importance of downstream sites and cofactors

We find that strong ChIP-chip sites co-localize with strong hERα consensus sites and detect nucleotide bias near hERα sites. The localization of ChIP-chip sites relative to annotated genes shows that weak sites are enriched near transcription start sites, while stronger sites show no positional bias. Assessing the relationship between binding configurations and expression phenotypes, we find binding sites downstream of the transcription start site (TSS) to be equally good or better predictors of hERα-mediated expression as upstream sites. The study of FOX and SP1 cofactor sites near hERα ChIP sites shows that induced genes frequently have FOX or SP1 sites. Finally we integrate these multiple datasets to define a high confidence set of primary hERα target genes.Our results support the model of long-range interactions of hERα with the promoter-bound cofactor SP1 residing at the promoter of hERα target genes. FOX motifs co-occur with hERα motifs along responsive genes. Importantly we show that the spatial arrangement of sites near the start sites and within the full transcript is important in determining response to estrogen signaling.Human estrogen receptor alpha (hERα) is an essential nuclear receptor regulating female development and reproductive functions. In the context of breast cancer, both hERα protein concentration and mRNA abundance have been shown to be associated with specific cancer sub-types and to influence survival rates [1-3]Estrogen receptor is known to bind DNA at estrogen responsive elements (EREs) and to activate transcription of its target genes, in particular early estrogen-responsive genes [4-7]. It was also shown that some hERα targets, such as c-Myc, lack the ERE, but instead contain AP1 or SP1 binding sites, which appear to be essential for transcription in vitro [5,8,9]. Studies about how the estrogen receptor eventually induces transcription of its target genes have lead to the identification of complex interactions between hERα and a large