Identifying estrogen receptor alpha target genes using integrated computational genomics and chromatin immunoprecipitation microarray.
The estrogen receptor alpha (ERalpha) 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 ERalpha loci were identified and the corresponding promoter sequences were analyzed by statistical pattern recognition and comparative genomics approaches. We found mouse counterparts for 63 of these loci and classified 42 (67%) as direct ERalpha 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 ERalpha promoters. Of the 27 loci upregulated in an ERalpha-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.
Jin
Victor X
VX
Human Cancer Genetics Program, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA.
Leu
Yu-Wei
YW
Liyanarachchi
Sandya
S
Sun
Hao
H
Fan
Meiyun
M
Nephew
Kenneth P
KP
Huang
Tim H-M
TH
Davuluri
Ramana V
RV
D000818:Animals; D001665:Binding Sites; D045744:Cell Line, Tumor; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D047628:Estrogen Receptor alpha / Q000378:metabolism*; D023281:Genomics / Q000379:methods*; D006801:Humans; D051379:Mice; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA
D047628:Estrogen Receptor alpha