title: Experimentally determined weight matrix definitions of the initiator and TBP binding site elements of promoters.
abstract: The basal elements of class II promoters are: (i) a-30 region, recognized by TATA binding protein (TBP); (ii) an initiator (Inr) surrounding the start site for transcription; (iii) frequently a downstream (+10 to +35) element. To determine the sequences that specify an Inr, we performed a saturation mutagenesis of the Inr of the SV40 major late promoter (SV40-MLP). The transcriptional activity of each mutant was determined both in vivo and in vitro. An excellent correlation between transcriptional activity and closeness of fit to the optimal Inr sequence, 5'-CAG/TT-3', was found to exist both in vivo and in vitro. Employing a neural network technique we generated from these data a weight matrix definition of an Inr that can be used to predict the activity of a given sequence as an Inr. Using saturation mutagenesis data of TBP binding sites we likewise generated a weight matrix definition of the -30 region element. We conclude the following: (i) Inrs are defined by the nucleotides immediately surrounding the transcriptional start site; (ii) most, if not all, Inrs are recognized by the same general transcription factor(s). We propose that the mechanism of transcription initiation is fundamentally conserved, with the formation of pre-initiation complexes involving the concurrent binding of general transcription factors to the -30, Inr and, possibly, downstream elements of class II promoters.
authors.affiliation: McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison 53706-1599, USA.
authors.forename: R J
authors.initials: RJ
authors.lastname: Kraus
authors.forename: E E
authors.initials: EE
authors.lastname: Murray
authors.forename: S R
authors.initials: SR
authors.lastname: Wiley
authors.forename: N M
authors.initials: NM
authors.lastname: Zink
authors.forename: K
authors.initials: K
authors.lastname: Loritz
authors.forename: G W
authors.initials: GW
authors.lastname: Gelembiuk
authors.forename: J E
authors.initials: JE
authors.lastname: Mertz
mesh_terms: D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D002460:Cell Line; D002522:Chlorocebus aethiops; D016384:Consensus Sequence; D004247:DNA; D004268:DNA-Binding Proteins / Q000378:metabolism*; D006367:HeLa Cells; D006801:Humans; D008969:Molecular Sequence Data; D016296:Mutagenesis; D010442:Peptide Chain Initiation, Translational; D011401:Promoter Regions, Genetic; D013539:Simian virus 40 / Q000235:genetics*; D016385:TATA Box; D035181:TATA-Box Binding Protein; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D004268:DNA-Binding Proteins; D035181:TATA-Box Binding Protein; D014157:Transcription Factors; D004247:DNA