Estrogen plays multiple roles in normal physiology and a pathologic one in breast cancer. The completion of the sequencing of the human genome has allowed the near-complete identification of the expressed regions of protein-coding genes, however, little is known concerning the organization of their cis-regulatory elements. In recently published studies we have completed chromosome-scale mapping of estrogen receptor (ER) association with the entire non-repetitive sequence of human chromosomes 21 and 22 by combining chromatin immunoprecipitation (ChIP) with high-density tiled microarrays (ChIP-chip). In these studies we find that ER binds selectively to a limited number of sites on these two chromosomes. Interestingly, the majority of these are at significant distances (>10kb) from the transcription start sites of estrogen-regulated genes. The unbiased sequence interrogation of these genuine ER binding sites suggests that ER binding often involves both estrogen response elements (ERE) and the presence of forkhead factor binding in close proximity. Furthermore, knockdown of the expression of the forkhead factor FoxA1 decreases both the association of ER with these sites and estrogen-induced gene expression. These studies, though limited to only two chromosomes and identifying only 57 binding sites, confirm the feasibility of defining the complete set of the predicted ~4000 ER binding sites across the entire human genome. We hypothesize that once all of the ER binding sites are identified that there will be distinct classes of ER targets based on the transcription factor motifs present within or adjacent to the ER binding regions. In addition, the extension of these studies to include the entire genome, should allow the study of genes both induced and repressed by estrogen. These hypotheses will be addressed in Aim 1. Our findings suggest the hypothesis that FoxA1 is necessary for defining a significant subset of ER targets in breast cancer cells. In addition we hypothesize that the different classes of ER targets defined in Aim 1 will represent different functional classes of target genes.
Aim 2 will test these hypotheses. Finally, the finding that most ER binding sites are distant from the mRNA start sites of the nearest genes raises the more general problem of how to assign putative cis-regulatory elements to specific target genes.
Aim 3 will address this problem.
|Bailey, Shannon T; Westerling, Thomas; Brown, Myles (2015) Loss of estrogen-regulated microRNA expression increases HER2 signaling and is prognostic of poor outcome in luminal breast cancer. Cancer Res 75:436-45|
|Jeselsohn, Rinath; Yelensky, Roman; Buchwalter, Gilles et al. (2014) Emergence of constitutively active estrogen receptor-? mutations in pretreated advanced estrogen receptor-positive breast cancer. Clin Cancer Res 20:1757-1767|
|He, Housheng Hansen; Meyer, Clifford A; Hu, Sheng'en Shawn et al. (2014) Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nat Methods 11:73-78|
|Buchwalter, Gilles; Hickey, Michele M; Cromer, Anne et al. (2013) PDEF promotes luminal differentiation and acts as a survival factor for ER-positive breast cancer cells. Cancer Cell 23:753-67|
|Bailey, Shannon T; Shin, Hyunjin; Westerling, Thomas et al. (2012) Estrogen receptor prevents p53-dependent apoptosis in breast cancer. Proc Natl Acad Sci U S A 109:18060-5|
|He, Housheng Hansen; Meyer, Clifford A; Chen, Mei Wei et al. (2012) Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res 22:1015-25|
|Villa, Alessandro; Della Torre, Sara; Stell, Alessia et al. (2012) Tetradian oscillation of estrogen receptor ? is necessary to prevent liver lipid deposition. Proc Natl Acad Sci U S A 109:11806-11|
|Tang, Qianzi; Chen, Yiwen; Meyer, Clifford et al. (2011) A comprehensive view of nuclear receptor cancer cistromes. Cancer Res 71:6940-7|
|Liu, Tao; Ortiz, Jorge A; Taing, Len et al. (2011) Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol 12:R83|
|Madak-Erdogan, Zeynep; Lupien, Mathieu; Stossi, Fabio et al. (2011) Genomic collaboration of estrogen receptor alpha and extracellular signal-regulated kinase 2 in regulating gene and proliferation programs. Mol Cell Biol 31:226-36|
Showing the most recent 10 out of 23 publications