Nucleic Acids Research, Vol 24, Issue 8 1531-1539, Copyright © 1996 by Oxford University Press
RJ Kraus, EE Murray, SR Wiley, NM Zink, K Loritz, GW Gelembiuk and JE Mertz
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.
ARTICLES
Experimentally determined weight matrix definitions of the initiator and TBP binding site elements of promoters
McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison 53706-1599, USA.
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