Functional significance of noncanonical sequence elements was examined using DNAse 1 footprinting data obtained for 33 different complexes of RNA polymerase with individual promoters. One of the strongest characteristics of the DNA in these complexes is the presence of the sites which reactivity against nuclease increases upon interaction with the enzyme (hyperreactive sites). The quantity of hyperreactive sites varies in different polymerase-promoter complexes, however their location is rather stable (near -47, -37 and -26/-25), indicating that the tight contacts with the enzyme, taking place at the opposite side of the helix, are made with the same face of DNA molecule [2]. We found that many elements, revealed by cluster analysis and typical for noncanonical promoter regions, are positioned near the hyperreactive sites. Thus, they can be involved in complex formation with the enzyme.
Those promoters which have high degree of homology with revealed sequence elements were selected as a representatives of corresponding promoter groups, and the presence of another sequence motifs in their structure was examined. Both positive and negative correlations were observed in some cases, nevertheless the degree of these interdependencies was low, indicating that a promoter can be created by different combination of signal elements.
This work was supported by the Russian Foundation for Basic Research
(grants N 97-04-49418 and 97-04-48404).