title: Relationship between estrogen receptor alpha location and gene induction reveals the importance of downstream sites and cofactors.
abstract: BACKGROUND
  To understand cancer-related modifications to transcriptional programs requires detailed knowledge about the activation of signal-transduction pathways and gene expression programs. To investigate the mechanisms of target gene regulation by human estrogen receptor alpha (hERalpha), we combine extensive location and expression datasets with genomic sequence analysis. In particular, we study the influence of patterns of DNA occupancy by hERalpha on expression phenotypes.
  
  
  RESULTS
  We find that strong ChIP-chip sites co-localize with strong hERalpha consensus sites and detect nucleotide bias near hERalpha 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 hERalpha-mediated expression as upstream sites. The study of FOX and SP1 cofactor sites near hERalpha 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 hERalpha target genes.
  
  
  CONCLUSIONS
  Our results support the model of long-range interactions of hERalpha with the promoter-bound cofactor SP1 residing at the promoter of hERalpha target genes. FOX motifs co-occur with hERalpha 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.
authors.affiliation: School of Life Sciences, Swiss Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland. Fabio.Parisi@med.nyu.edu
authors.forename: Fabio
authors.initials: F
authors.lastname: Parisi
authors.forename: Bernhard
authors.initials: B
authors.lastname: Sonderegger
authors.forename: Pratyaksha
authors.initials: P
authors.lastname: Wirapati
authors.forename: Mauro
authors.initials: M
authors.lastname: Delorenzi
authors.forename: Felix
authors.initials: F
authors.lastname: Naef
mesh_terms: D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D047628:Estrogen Receptor alpha / Q000235:genetics* / Q000378:metabolism; D051858:Forkhead Transcription Factors / Q000378:metabolism; D005786:Gene Expression Regulation; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D016329:Sp1 Transcription Factor / Q000378:metabolism; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
chemical_list: D047628:Estrogen Receptor alpha; D051858:Forkhead Transcription Factors; D016329:Sp1 Transcription Factor
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