Identification of Estrogen-responsive Genes Using a Genome-wide Analysis of Promoter Elements for Transcription Factor Binding Sites

Abstract

We developed a pipeline to identify novel genes regulated by the steroid hormone-dependent transcription factor, estrogen receptor, through a systematic analysis of upstream regions of all human and mouse genes. We built a data base of putative promoter regions for 23,077 human and 19,984 mouse transcripts from National Center for Biotechnology Information annotation and 8793 human and 6785 mouse promoters from the Data Base of Transcriptional Start Sites. We used this data base of putative promoters to identify potential targets of estrogen receptor by identifying estrogen response elements (EREs) in their promoters. Our program correctly identified EREs in genes known to be regulated by estrogen in addition to several new genes whose putative promoters contained EREs. We validated six genes (KIAA1243, NRIP1, MADH9, NME3, TPD52L, and ABCG2) to be estrogen-responsive in MCF7 cells using reverse transcription PCR. To allow for extensibility of our program in identifying targets of other transcription factors, we have built a Web interface to access our data base and programs. Our Web-based program for Promoter Analysis of Genome, PAGen@UIC, allows a user to identify putative target genes for vertebrate transcription factors through the analysis of their upstream sequences. The interface allows the user to search the human and mouse promoter data bases for potential target genes containing one or more listed transcription factor binding sites (TFBSs) in their upstream elements, using either regular expression-based consensus or position weight matrices. The data base can also be searched for promoters harboring user-defined TFBSs given as a consensus or a position weight matrix. Furthermore, the user can retrieve putative promoter sequences for any given gene together with identified TFBSs located on its promoter. Orthologous promoters are also analyzed to determine conserved elements.Estrogens play a critical role in vertebrate reproduction, especially in the development of female sex organs (1). The bulk of estrogen signaling is controlled by estrogen receptors ␣ and ␤ (ER␣ 1 and ER␤), members of the nuclear receptor superfamily (2) of ligand-inducible transcription factors. ER␣ and ER␤ bind to the estrogen response element (ERE) on the promoters of the genes they regulate. The ERE is a palindrome of RG-GTCA motifs separated by 3 bp (3). These elements are bound by ER dimers, with one receptor binding each motif. The sequence and spatial organization of the ERE is important for the specificity of binding. Although a crystal structure of the DNAbound ER is available (4), the unexpected diversity of DNA response elements mediating transcriptional regulation by ERs has made finding EREs in the genome very difficult. In fact, none of the typical estrogen-responsive genes have consensus EREs.

Human Multidrug Resistance ABCB and ABCG Transporters: Participation in a Chemoimmunity Defense System

“…The same element has been found by a systematic genome-wide bioinformatic study by analyzing promoter elements for transcription factor binding sites with the aim of identifying estrogen-responsive genes (169). However, the regulation of ABCG2 seems to be cell line specific, because it is actually downregulated following estrogen treatment in ER-positive MCF7 cells (169). Moreover, as mentioned below, estrogen regulation of ABCG2 may be mostly of posttranslational nature.…”

Single-step doxorubicin-selected cancer cells overexpress the ABCG2 drug transporter through epigenetic changes

“…Thus, this transporter is unlikely to be associated with drug resistance in the single-step-selected clones. Using PAGen@UIC (www.uic.edu/pharmacy/depts/pmpcpd/pagen/), we found that there are 11 predicted transcription factors that have binding sites on the promoters of both ABCG2 and ABCC4 (Kamalakaran et al, 2005). Thus, it is possible that the coordinate overexpression of both transporters may be due to an effect of common transcription factors.…”

Regulation of the Neuronal Proteasome by Zif268 (Egr1)

“…Bioinformatic analysis of gene promoters, using software trained to identify consensus TF recognition sequences, has proved of great use in detecting functional TF binding sites (Tullai et al, 2004;Chowdhary et al, 2005;Kamalakaran et al, 2005;Xie et al, 2005;Zhang et al, 2005). To assess the likelihood that the identified genes are direct targets of Zif268, we assessed the abundance of consensus EREs in the genomic region 1 kb upstream of the TSS of 24 proteasome-related genes identified as potential Zif268 targets compared with 20 randomly selected genes (see Materials and Methods) (Table 2), using the program MatInspector (Quandt et al, 1995).…”