title: Linking DNA-binding proteins to their recognition sequences by using protein microarrays.
abstract: Analyses of whole-genome sequences and experimental data sets have revealed a large number of DNA sequence motifs that are conserved in many species and may be functional. However, methods of sufficient scale to explore the roles of these elements are lacking. We describe the use of protein arrays to identify proteins that bind to DNA sequences of interest. A microarray of 282 known and potential yeast transcription factors was produced and probed with oligonucleotides of evolutionarily conserved sequences that are potentially functional. Transcription factors that bound to specific DNA sequences were identified. One previously uncharacterized DNA-binding protein, Yjl103, was characterized in detail. We defined the binding site for this protein and identified a number of its target genes, many of which are involved in stress response and oxidative phosphorylation. Protein microarrays offer a high-throughput method for determining DNA-protein interactions.
authors.affiliation: Washington University School of Medicine, 4444 Forest Park Boulevard, St. Louis, MO 63108, USA.
authors.forename: Su-Wen
authors.initials: SW
authors.lastname: Ho
authors.forename: Ghil
authors.initials: G
authors.lastname: Jona
authors.forename: Christina T L
authors.initials: CT
authors.lastname: Chen
authors.forename: Mark
authors.initials: M
authors.lastname: Johnston
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D040081:Protein Array Analysis / Q000379:methods*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D004268:DNA-Binding Proteins; C500382:GSM1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors; D004247:DNA