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Promoter sequences of Escherichia coli were compiled and their transcribed regions characterized by site-specific cluster analysis. Here we report that transcribed regions contain a non-random distribution of A/T tracts with strongly preferred positions at 6 +/- 3, 23 +/- 3, 40 +/- 2 and 56 +/- 2. The maxima of this distribution follow an unusual periodicity (approximately 17 bp) and are in phase with important promoter elements involved in interaction with RNA polymerase, while the value of periodicity numerically fits the spacer length between the canonical -35 and -10 elements. The possible functional significance of this newly described feature is discussed in the context of promoter clearance and transcription pausing.

Proximal transcribed regions of bacterial promoters have a non-random distribution of A/T tracts