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Interrogating the genome to understand oestrogen-receptor-mediated transcription

Published online by Cambridge University Press:  01 April 2008

Sara C. Dietz
Affiliation:
Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
Jason S. Carroll*
Affiliation:
Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
*
*Corresponding author: Jason S. Carroll, Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK. Tel:  + 44 (0)1223 404510; Fax:  + 44 (0)1223 404199; E-mail: jason.carroll@cancer.org.uk
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Abstract

Defining transcription mediated by the oestrogen (estrogen) receptor (ER) in breast cancer cell models has been an area of interest for many years. Initial studies focused on promoter regions of putative target genes and revealed significant insight into the basis of ER binding to DNA. More recently, the complexities of ER transcription are starting to become apparent. It is now clear that ER can regulate gene targets from significant distances and that cooperating transcription factors play an integral role in ER activity. It is also clear that the sequence information defining an in vivo ER-binding site is more complicated than initially thought. However, contemporary genomic tools based on chromatin immunoprecipitation (ChIP) – such as ChIP-on-chip and ChIP–sequencing – and gene expression profiling have allowed us to redefine the underlying properties of ER biology on a genomic scale. The advances in technology that have permitted a better understanding of how and where ER can bind to DNA are discussed in this review. The possible clinical implications of these findings for understanding the role of oestrogen in breast cancer are also briefly considered.

Information

Type
Review Article
Copyright
Copyright © Cambridge University Press 2008
Figure 0

Figure 1.A basic schematic model of oestrogen action. Oestrogen (E2) is a steroid and as such can diffuse into cells readily, where it associates with an oestrogen receptor (ER)-α homodimer. This complex can subsequently find specific motifs (oestrogen-responsive elements; EREs) within the DNA and physically bind to those regions of the DNA to induce transcription. However, the ER has also been shown to bind to DNA via motifs that are specific to other transcription factors.

Figure 1

Figure 2.Cyclic association of the oestrogen receptor transcription complex with a promoter. (a) Chromatin immunoprecipitation (ChIP) of the oestrogen receptor (ER) and suspected cofactors on the cathepsin D promoter after increasing periods of oestrogen stimulation reveals cyclic association of the transcription complex, supporting (b) a model whereby cofactors associate with ER to potentially regulate chromatin structure. In this ChIP approach, MCF-7 breast epithelial cells are deprived of steroids to induce cell cycle arrest, and then transcriptional events are synchronised by the addition of oestrogen for increasing time periods. The cells are crosslinked and the chromatin is collected and sonicated. Precipitation by an antibody against the protein of interest enriches for DNA associated with the protein. DNA is purified and PCR is performed of a known binding site within a promoter of a regulated gene. Abbreviations: AcH, acetylated histone; AIB1, amplified in breast cancer 1; CBP, CREB-binding protein; p/CAF, p300/CREB-binding protein associated factor; Pol II, RNA polymerase II. The ChIP data in part a are reprinted from Ref. 18 (© 2000 Elsevier), with permission from Elsevier.

Figure 2

Figure 3.Schematic of oestrogen receptor ChIP-on-chip procedure. MCF-7 cells are deprived of hormones to induce cell cycle arrest, and transcription is subsequently reinitiated by adding oestrogen. Chromatin is then crosslinked by adding formaldehyde and the chromatin sheared into smaller fragments by sonication. The chromatin is incubated with an antibody against the oestrogen receptor (ER) and the chromatin precipitated from background: this enriches for fragments of chromatin that are bound by the ER. The chromatin is purified and the DNA is validated, amplified and labelled. Labelled DNA is hybridised to microarrays. Total genomic DNA (input) is also included as a control and ER-binding sites are determined as regions of the genome enriched above the input background levels. Increased binding of DNA to specific probes is reflected as increased signal on the microarray.

Figure 3

Figure 4.Graphical representation of binding sites of the oestrogen receptor on chromosome 21, as determined by ChIP-on-chip. The oestrogen receptor (ER) binds to a limited number of sites, most of which are distant from promoter regions. ER ChIP-on-chip was performed by stimulating cells with oestrogen, crosslinking the chromatin and immunoprecipitating the ER. The chromatin was hydridised to tiling microarrays covering all the nonrepetitive sequence from chromosomes 21 and 22 at 35 bp resolution (Ref. 45). This means that a probe existed every 35 bp along the nonrepetitive region of the chromosome. The blue bars indicate gene locations; the black bars represent predicted ER-binding sites in the form of an oestrogen-responsive element (ERE); the red bars represent the experimentally defined in vivo ER-binding sites. The numbers under the chromosome represent base pairs. These data confirm that ER binds only to a small fraction of predicted binding sites that contain an ERE and therefore that a majority of EREs are not functional. Below is an expanded view of the TFF1 gene (in its genuine 3′ to 5′ orientation), showing ER binding at the promoter and an upstream enhancer. This gene represents one of the few ER-binding sites at a promoter region. A second binding site exists upstream of the TFF1 gene and functions as an enhancer of TFF1 transcription, despite the fact that it is located within an adjacent gene, TMPRSS2.

Figure 4

Table 1.The benefits and disadvantages of ChIP-on-chip and ChIP–sequencing to define transcription factor binding events