Estrogen receptor α target genes: The role of integrated computational genomics and chromation immunoprecipitation microarray

Objective - To identify these promoter sequences involve in regulating gene expression by direct or indirect methods. Design - A combination of a systematic computational approach and microaray-based ChIP-on-chip for the genome-wide identification of ERα target genes. Method - We conducted a genome-wide screening with a novel microarray technique called ChIP-on-chip. A set of 70 candidate ERα loci was identified and the corresponding promoter sequences were analysed by statistical pattern recognition and comparative genomics approaches. Results - We found mouse counterparts for 63 of these loci and classified 42 (67%) as direct ERα targets using classification and regression tree (CART) statistical model which involves position weight matrix and human-mouse sequence similarity scores as model parameters. The remaining genes were considered to be indirect targets. To validate this computational prediction, we conducted an additional ChIP-on-chip assay that identified acetylated chromatin components in active ERα promoters. Of the 27 loci upregulated in and ERα-positive breast cancer cell line, 20 having mouse counterparts were correctly predicted by CART. Discussion and Conclusion - This integrated approach, therefore, sets a paradigm in which the iterative process of model refinement and experimental verification will continue until an accurate production of promoter target sequences is derived.