Genome-wide identification of peroxisome proliferator response elements using integrated computational genomics.
Peroxisome proliferator-activated receptor (PPAR) agonists are currently used therapeutically in humans, even though many of their direct gene targets are unknown. Because PPARs can directly regulate gene expression through peroxisome proliferator response elements (PPREs), we pursued the computational prediction of PPREs on a genome-wide scale. Contrary to current hypotheses, PPREs are not isotype-specific, nor do flanking nucleotides confer additional information. However, a position weight matrix-based search for PPREs within upstream conserved elements yielded sufficient selectivity for a genome-wide search. Additionally, a novel motif occurring with greater prevalence than PPREs was revealed. Microarray and gene ontology analyses further validated our search technique and provided new functional clusters of genes that were not previously known to be directly regulated by PPARs (e.g., chromatin remodeling, DNA damage response, Wnt, and mitogen-activated protein kinase signaling). This first genome-wide library of high-confidence predicted PPAR target genes will be a valuable resource to PPAR biologists.
Lemay
Danielle G
DG
United States Department of Agriculture, Agricultural Research Service, Western Human Nutrition Research Center, and Department of Nutrition, University of California-Davis, 95616, USA.
Hwang
Daniel H
DH
D000818:Animals; D019295:Computational Biology; D017124:Conserved Sequence; D004247:DNA / Q000235:genetics; D005786:Gene Expression Regulation; D015723:Gene Library; D015894:Genome, Human; D023281:Genomics / Q000379:methods* / Q000706:statistics & numerical data; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D047492:Peroxisome Proliferator-Activated Receptors / Q000235:genetics*; D051381:Rats
D047492:Peroxisome Proliferator-Activated Receptors; D004247:DNA