Identifying estrogen receptor target genes using integrated computational genomics and chromatin immunoprecipitation microarray

V. X. Jin
2004 Nucleic Acids Research  
The estrogen receptor a (ERa) regulates gene expression by either direct binding to estrogen response elements or indirect tethering to other transcription factors on promoter targets. To identify these promoter sequences, we conducted a genome-wide screening with a novel microarray technique called ChIP-on-chip. A set of 70 candidate ERa loci were identified and the corresponding promoter sequences were analyzed by statistical pattern recognition and comparative genomics approaches. We found
more » ... use counterparts for 63 of these loci and classified 42 (67%) as direct ERa 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 ERa promoters. Of the 27 loci upregulated in an ERa-positive breast cancer cell line, 20 having mouse counterparts were correctly predicted by CART. This integrated approach, therefore, sets a paradigm in which the iterative process of model refinement and experimental verification will continue until an accurate prediction of promoter target sequences is derived.
doi:10.1093/nar/gkh1005 pmid:15608294 pmcid:PMC545447 fatcat:n6h5qhjijbaqtbvb5mgm7vfhaa