title: Prediction and experimental validation of novel STAT3 target genes in human cancer cells.
abstract: The comprehensive identification of functional transcription factor binding sites (TFBSs) is an important step in understanding complex transcriptional regulatory networks. This study presents a motif-based comparative approach, STAT-Finder, for identifying functional DNA binding sites of STAT3 transcription factor. STAT-Finder combines STAT-Scanner, which was designed to predict functional STAT TFBSs with improved sensitivity, and a motif-based alignment to minimize false positive prediction rates. Using two reference sets containing promoter sequences of known STAT3 target genes, STAT-Finder identified functional STAT3 TFBSs with enhanced prediction efficiency and sensitivity relative to other conventional TFBS prediction tools. In addition, STAT-Finder identified novel STAT3 target genes among a group of genes that are over-expressed in human cancer cells. The binding of STAT3 to the predicted TFBSs was also experimentally confirmed through chromatin immunoprecipitation. Our proposed method provides a systematic approach to the prediction of functional TFBSs that can be applied to other TFs.
authors.affiliation: Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea.
authors.forename: Young Min
authors.initials: YM
authors.lastname: Oh
authors.forename: Jong Kyoung
authors.initials: JK
authors.lastname: Kim
authors.forename: Yongwook
authors.initials: Y
authors.lastname: Choi
authors.forename: Seungjin
authors.initials: S
authors.lastname: Choi
authors.forename: Joo-Yeon
authors.initials: JY
authors.lastname: Yoo
mesh_terms: D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D016678:Genome; D006801:Humans; D051379:Mice; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D050796:STAT3 Transcription Factor / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D050796:STAT3 Transcription Factor; C494086:STAT3 protein, human; D014157:Transcription Factors