title: Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.
abstract: We developed a new DNA microarray-based technology, called protein binding microarrays (PBMs), that allows rapid, high-throughput characterization of the in vitro DNA binding-site sequence specificities of transcription factors in a single day. Using PBMs, we identified the DNA binding-site sequence specificities of the yeast transcription factors Abf1, Rap1 and Mig1. Comparison of these proteins' in vitro binding sites with their in vivo binding sites indicates that PBM-derived sequence specificities can accurately reflect in vivo DNA sequence specificities. In addition to previously identified targets, Abf1, Rap1 and Mig1 bound to 107, 90 and 75 putative new target intergenic regions, respectively, many of which were upstream of previously uncharacterized open reading frames. Comparative sequence analysis indicated that many of these newly identified sites are highly conserved across five sequenced sensu stricto yeast species and, therefore, are probably functional in vivo binding sites that may be used in a condition-specific manner. Similar PBM experiments should be useful in identifying new cis regulatory elements and transcriptional regulatory networks in various genomes.
authors.affiliation: Division of Genetics, Department of Medicine, Harvard Medical School; Boston; Massachusetts 02115, USA. mlbulyk@receptor.med.harvard.edu
authors.forename: Sonali
authors.initials: S
authors.lastname: Mukherjee
authors.forename: Michael F
authors.initials: MF
authors.lastname: Berger
authors.forename: Ghil
authors.initials: G
authors.lastname: Jona
authors.forename: Xun S
authors.initials: XS
authors.lastname: Wang
authors.forename: Dale
authors.initials: D
authors.lastname: Muzzey
authors.forename: Michael
authors.initials: M
authors.lastname: Snyder
authors.forename: Richard A
authors.initials: RA
authors.lastname: Young
authors.forename: Martha L
authors.initials: ML
authors.lastname: Bulyk
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D002843:Chromatin / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D015966:Gene Expression Regulation, Fungal; D047468:Immunoprecipitation; D040081:Protein Array Analysis / Q000379:methods*; D013045:Species Specificity; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D015003:Yeasts
chemical_list: D002843:Chromatin; D014157:Transcription Factors