Genome-wide identification of peroxisome proliferator response elements using integrated computational genomics

Danielle G. Lemay, Daniel H. Hwang

Research output: Contribution to journalArticle

103 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1583-1587
Number of pages5
JournalJournal of Lipid Research
Volume47
Issue number7
DOIs
StatePublished - 2006
Externally publishedYes

Fingerprint

Peroxisome Proliferators
Peroxisome Proliferator-Activated Receptors
Response Elements
Genomics
Genes
Genome
Position-Specific Scoring Matrices
Gene Ontology
Chromatin Assembly and Disassembly
Genomic Library
Multigene Family
Mitogen-Activated Protein Kinases
DNA Damage
Microarrays
Gene expression
Nucleotides
Chromatin
Ontology
Gene Expression
DNA

Keywords

  • Conserved elements
  • PACM
  • Peroxisome proliferator-activated receptor
  • Target genes

ASJC Scopus subject areas

  • Endocrinology

Cite this

Genome-wide identification of peroxisome proliferator response elements using integrated computational genomics. / Lemay, Danielle G.; Hwang, Daniel H.

In: Journal of Lipid Research, Vol. 47, No. 7, 2006, p. 1583-1587.

Research output: Contribution to journalArticle

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