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MUST WATCH Building confidenceWhen 'one turned into two''Very, very rewarding'See the latest news and share your comments with CNN Health on Facebook and Twitter.All prices list below are price per month + tax Regular Monthly Price $75.85 Regular Monthly Price $85.85 Regular Monthly Price $106.35 Regular Monthly Price $115.35 Regular Monthly Price $116.50 Regular Monthly Price $115.40 Regular Monthly Price $129.95 Regular Monthly Price $139.95 Regular Monthly Price $149.75 Regular Monthly Price $133.95 Regular Monthly Price $155.95 Regular Monthly Price $181.95 Regular Monthly Price $249.55 Regular Monthly Price $269.90 Regular Monthly Price $212.95 Regular Monthly Price $322.35 Regular Monthly Price $348.35 Regular Monthly Price $348.95Volume 1, Issue 2, September 2007, Pages 138–143 The estrogen receptor (ER) is a ligand inducible transcription factor that regulates a large number of target genes.




These targets are particularly relevant in breast cancer, where the sensitivity of the tumor to estrogens determines whether the patients can be treated with endocrine therapy such as tamoxifen. Identifying genomic ER targets is a daunting task. Quantifying expression levels of suspected target genes after estradiol stimulation or, more recently, using expression microarrays to this effect will reveal which genes are regulated by estradiol, however, without discriminating between direct and indirect targets. The identification of the palindromic sequence that defines the estrogen responsive element (ERE) allows for the in silico discovery of putative ER targets in the genome. However the ER can also bind imperfect EREs and half sites, and can bind indirectly via other factors. Chromatin immunoprecipitation (ChIP) can yield all ER genomic target sites. Coupling of ChIP with genome-wide tiling arrays allows for the genome-wide unbiased identification of direct ER target sequences.In 1896 Beatson observed that removing the ovaries could lead to remission of breast cancer (Beatson, 1896).




Although at that time hormones were not yet discovered, his experiments were the first to connect estrogens with breast cancer. More than 60 years later it was demonstrated that estrogens were retained in target tissues (Jensen and Jacobson, 1962), laying the foundation for the subsequent identification of steroid receptors. Indeed, in 1968 O'Malley described that changes in gene expression occurred after estrogen stimulation, indicating estrogen receptor (ER) functions as a transcription factor (O'Malley et al., 1968). Soon after, a protein that specifically bound estrogens was found in breast tumors, and its quantity could predict the response of these tumors to endocrine disruption (Jensen et al., 1971 and McGuire, 1973). With the cloning of the ER in 1986 (Green et al., 1986 and Greene et al., 1986) and subsequent identification of its functional domains the role for the ER as a ligand dependent transcription factor became apparent (Green et al., 1986, Greene et al., 1986 and Kumar et al., 1987).




The ER is a member of the superfamily of nuclear receptors, which are structurally related ligand-inducible transcription factors, including steroid receptors (SRs), thyroid/retinoids receptors (TR, RARs and RXRs), vitamin D receptors (VDR), LXR, PPARs, and orphan receptors for which no ligand has been yet identified. After binding of estrogen to the estrogen-binding site on the ER, the receptor dimerizes, translocates to the nucleus of the target cell, and binds to specific regions on chromatin, the so-called estrogen response elements (EREs). In addition, the ER can interact with other transcription factors, SP-1, AP-1 and NF-κB bound to their regulatory regions. These interactions, and the specific genes that are regulated by the interaction of the ER with chromatin regions have been subject to research over the years. This review will focus on the methods and research done to identify ER targets genes.Elucidating ER target genes has for long been done on a gene-by-gene basis, measuring the effect of estrogen stimulation on the expression of a single gene.




By differentially screening cDNA libraries of induced and non-induced cells several target genes have been discovered, e.g. pS2/TFF1 (Brown et al., 1984 and Jakowlew et al., 1984). Recently, investigation of global expression changes upon estradiol induction by SAGE or microarray has identified many ER target genes (Charpentier et al., 2000, Cunliffe et al., 2003, Frasor et al., 2003, Inoue et al., 2002 and Seth et al., 2002). Interestingly, these global expression experiments indicated that around half of ER target genes are down regulated upon induction with estrogen. Many of the down-regulated genes are known to inhibit the cell cycle, are pro-apoptotic or are cytokines and growth factors that inhibit proliferation. This is in agreement with the view that estrogen promotes cell survival by down regulating pro-apoptotic genes. Although global expression profiling provides a wealth of information on estrogen induced gene expression, it cannot distinguish between direct and indirect ER targets, i.e. genes that are regulated by other genes that are directly regulated by the ER.




For this, protein synthesis inhibitors cycloheximide or puromycin can be used, although unspecific effects of these drugs cannot be excluded. All targets that are regulated by estrogens in the presence of protein synthesis inhibitors should be bona fide direct ER targets. Soulez and Parker used this to confirm that the P450-IIB enzyme was a direct target for the ER in ZR75-1 cells (Soulez and Parker, 2001), and Wang et al. (2004) found EEIG1 to be a direct ER target in MCF7 cells. To the best of our knowledge, no genome-wide expression profile has been performed in breast cancer cells in the presence of protein synthesis inhibitors.Klein-Hitpass et al. (1986) identified an estrogen response element in the Xenopus vittelogenin A2 gene in 1986. They showed that this element functions in humans and defined a palindromic sequence (5′-GGTCACAGTGACC-3′) as the core ERE ( Klein-Hitpass et al., 1986). With the sequencing of the human genome it became possible to search in silico for the presence of EREs.




These computational approaches have been used to identify ER target genes with limited success. From an extensive study where 71,119 EREs were identified, only 3 were perfect ERE palindromes ( Bourdeau et al., 2004). By narrowing down to promoter regions still 12,515 EREs were identified and by including conservation with mouse, 660 EREs remained of which several could be validated. Other authors have used similar approaches (Kamalakaran et al., 2005). As the ER can bind imperfect EREs and half sites, it is computationally very difficult to distinguish between real binding sites and noise. In addition, ER can bind indirectly via other factors, which cannot be assessed using this approach.Chromatin immunoprecipitation (ChIP) is a new and very powerful technique by which transcription factor/co-factor occupancy of a given locus can be determined in its chromatin context in vivo. In brief, protein and DNA are cross-linked in the living cell using formaldehyde, chromatin is fragmented, and the transcription (co)factor of interest is immunoprecipitated with specific antibodies.

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