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

Sitharthan Kamalakaran,Senthil K Radhakrishnan,William T Beck

doi:10.1074/jbc.m409176200

Sitharthan Kamalakaran, Senthil K Radhakrishnan + Show 1 more

Open Access

https://doi.org/10.1074/jbc.m409176200

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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.

Highlights

Estrogens play a critical role in vertebrate reproduction, especially in the development of female sex organs [1]
We used the TRANSFAC data base [18, 19] of DNA binding profiles of eukaryotic transcription factors to build a regular expression (RegEx)-based consensus binding set and a position weight matrix profile for various vertebrate transcription factors. These were run against the data base of human and mouse promoters
We established a “PAGen data base” whereby each annotated gene is defined by a set of putative transcription factor binding sites (TFBSs) located in its putative promoter regions (PPRs)

Summary

Introduction

Estrogens play a critical role in vertebrate reproduction, especially in the development of female sex organs [1]. 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.

Results

Conclusion