Genomic Analyses of Transcription Factor Binding, Histone Acetylation, and Gene Expression Reveal Mechanistically Distinct Classes of Estrogen-Regulated Promoters

Abstract

To explore the global mechanisms of estrogen-regulated transcription, we used chromatin immunoprecipitation coupled with DNA microarrays to determine the localization of RNA polymerase II (Pol II), estrogen receptor alpha (ER␣), steroid receptor coactivator proteins (SRC), and acetylated histones H3/H4 (AcH) at estrogen-regulated promoters in MCF-7 cells with or without estradiol (E2) treatment. In addition, we correlated factor occupancy with gene expression and the presence of transcription factor binding elements. Using this integrative approach, we defined a set of 58 direct E2 target genes based on E2-regulated Pol II occupancy and classified their promoters based on factor binding, histone modification, and transcriptional output. Many of these direct E2 target genes exhibit interesting modes of regulation and biological activities, some of which may be relevant to the onset and proliferation of breast cancers. Our studies indicate that about one-third of these direct E2 target genes contain promoter-proximal ER␣-binding sites, which is considerably more than previous estimates. Some of these genes represent possible novel targets for regulation through the ER␣/AP-1 tethering pathway. Our studies have also revealed several previously uncharacterized global features of E2-regulated gene expression, including strong positive correlations between Pol II occupancy and AcH levels, as well as between the E2-dependent recruitment of ER␣ and SRC at the promoters of E2-stimulated genes. Furthermore, our studies have revealed new mechanistic insights into E2-regulated gene expression, including the absence of SRC binding at E2-repressed genes and the presence of constitutively bound, promoter-proximally paused Pol IIs at some E2-regulated promoters. These mechanistic insights are likely to be relevant for understanding gene regulation by a wide variety of nuclear receptors.

Differential modulation of glucocorticoid and progesterone receptor transactivation

“…However, the GME appears to be equally active with both endogenous and synthetic reporter genes Szapary et al, 1992;Collier et al, 1996). Furthermore, it is clear from microarray studies that endogenous genes yield a spectrum of responses that resist generalization (Mittelstadt and Ashwell, 2003;Rogatsky et al, 2003;Donn et al, 2007;Kininis et al, 2007). Therefore, the present results establish that various factors can unequally alter the transcription properties of PR vs. GR in a model system that most likely is recapitulated by some endogenous regulated genes.…”

Garcinol, an Acetyltransferase Inhibitor, Suppresses Proliferation of Breast Cancer Cell Line MCF-7 Promoted by 17β-Estradiol

“…With the activation of cell signaling pathway, histone acetylation levels of nuclear receptors (such as ER, GR, RAR, VDR) target genes are significantly increased, thus activating gene transcription upon hormone induction. Genomic analyses of transcription factor binding indicate a remarkable positive correlation between the recruitment of Pol II at the promoters of E 2 -stimulated genes and the acetylated histone levels (Kininis et al, 2007). Using a well-established ACI rat model, Kristy R et al identified morphological and epigenetic changes in the mammary gland tissue after exposure to constitutively elevated estrogen levels, and found that progressive hyperproliferative changes were paralleled by epigenetic disturbances, which demonstrates that the hyperacetylation of histone induced by estrogen has a significant role in the early stage of breast cancer development (Kutanzi et al, 2010).…”

“…Estrogen is an important factor promoting cell proliferation in estrogen receptor (ER) positive breast cancer, which is associated with abnormal changes in acetylation levels in current study (Kininis et al, 2007). Estrogen may affect the acetylation levels of histones or nonhistones of oncogenes, thus boost oncogene expression, tumor cell transformation, accelerate proliferation and inhibit apoptosis.…”

Membrane-initiated estrogen signaling in hypothalamic neurons

“…However, recently the FASEB steroid signaling work group suggested that "membrane-initiated steroid signaling" and "nuclear-initiated steroid signaling" are more appropriate terminologies (Hammes and Levin, 2007). The nuclear-effects on a variety of tissues that involves gene stimulation as well as gene repression (Herbison, 1998, Couse and Korach, 1999, Nilsson et al, 2001, Stossi et al, 2006, Kininis et al, 2007. In general, this "classical" signaling pathway of estrogen involves steroid-dependent formation of nuclear estrogen receptor homo-or heterodimers and the subsequent binding of this complex with a unique DNA sequence known as an estrogen response element (ERE), in E2-responsive gene promoters (O'Malley and Tsai, 1992, Muramatsu and Inoue, 2000, Gruber et al, 2004.…”