Genome-Wide Dynamics of Chromatin Binding of Estrogen Receptors α and β: Mutual Restriction and Competitive Site Selection

Abstract

Estrogen receptors ERalpha and ERbeta, members of the nuclear receptor superfamily, exert profound effects on the gene expression and biological response programs of their target cells. Herein, we explore the dynamic interplay between these two receptors in their selection of chromatin binding sites when present separately or together in MCF-7 breast cancer cells. Treatment of cells (containing ERalpha only, ERbeta only, or ERalpha and ERbeta) with estradiol or ER subtype-selective ligands was followed by chromatin immunoprecipitation analysis with a custom-designed tiling array for ER binding sites across the genome to examine the effects of ligand-occupied and unoccupied ERalpha and ERbeta on chromatin binding. There was substantial overlap in binding sites for these estradiol-liganded nuclear receptors when present alone, but many fewer sites were shared when both ERs were present. Each ER restricted the binding site occupancy of the other, with ERalpha generally being dominant. Binding sites of both receptors were highly enriched in estrogen response element motifs, but when both ERs were present, ERalpha displaced ERbeta, shifting it into new sites less enriched in estrogen response elements. Binding regions of the two ERs also showed differences in their enrichments for other transcription factor binding motifs. Studies with ER subtype-specific ligands revealed that it was the liganded subtype that principally determined the spectrum of chromatin binding. These findings highlight the dynamic interplay between the two ERs in their selection of chromatin binding sites, with competition, restriction, and site shifting having important implications for the regulation of gene expression by these two nuclear receptors.

Genome-Wide Mapping of Estrogen Receptor-β–Binding Regions Reveals Extensive Cross-Talk with Transcription Factor Activator Protein-1

“…Fifty-one percent (2,439 sites) of our less stringent set of ERβ sites and 76% (1,112 sites) of our stringent set of ERβ sites, respectively, were also identified as ERα-binding sites by Carroll and colleagues (14). More recently, Charn and colleagues (26), using a custom-designed tiling array that contains approximately 77,000 genomic regions, have identified 1,744 ERβ-binding sites. As shown in Fig.…”

“…B, the distribution and occurrence of ERE-like sites, AP-1-like sites, and Forkhead-like sites within the identified ERβ-binding sites. C, Venn diagram of the overlap between the 4,766 sites or 1,457 sites derived using less or more strict inclusion criteria in this study and the 5,782 ERα sites discovered by Carroll and colleagues (14) or the 1,744 ERβ sites discovered by Charn and colleagues (26), respectively. ChIP-on-chip data of 5,782 ERα sites by Carroll and colleagues (14) was downloaded (44).…”

“…We compared our ERβ cistromes, 4,766 sites or 1,457 sites derived using less or more strict inclusion criteria, respectively, with the published ERα cistrome of 5,782 binding sites (14) and the recently published ERβ cistrome of 1,744 sites (26), all derived from MCF7 cells (Fig. 2C).…”

A bi-faceted role of estrogen receptor β in breast cancer

“…Four publications to date document genome binding (cistrome) studies of overexpressed ERb1 in MCF7 breast cancer cells in culture , Charn et al 2010, Grober et al 2011. These studies differ somewhat in their conclusions, although a common finding is that a reasonable degree of overlap exists between the cistrome of ERb1 and ERa at least in MCF7 cells.…”

“…Analysis of the ERb1 target sequences within the genome identified ERE or half ERE binding sites as generally enriched, but each of the studies identifies distinct enrichment of other motifs not ERE related. The reasons for the differences, in these as well as those studies looking only at gene expression changes, may be due to the different experimental design: for example, in some cases, stable inducible overexpression of ERb1 in MCF7 or T47D (Williams et al 2008) cells was used, another used stable overexpression of ERb1 in MCF7 cells (Grober et al 2011) and others used transient adenoviral mediated ERb1 overexpression (Paruthiyil et al 2004, Chang et al 2006, Charn et al 2010. Furthermore, the resulting levels of ERb1 overexpression may differ significantly among the studies.…”