Experimentally determined weight matrix definitions of the initiator and TBP binding site elements of promoters

Richard J. Kraus, Elizabeth E. Murray, Steven R. Wiley, Nancy M. Zink, Karla Loritz, Gregory W. Gelembiuk, Janet E. Mertz

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)1531-1539
Number of pages9
JournalNucleic acids research
Issue number8
StatePublished - 1996
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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