The yeast RNA polymerase I promoter: ribosomal DNA sequences involved in transcription initiation and complex formation in vitro.

Using an in vitro transcription system for Saccharomyces cerevisiae RNA polymerase I, we have analyzed Pol I promoter deletion mutants and mapped the boundaries of the promoter between positions -155 and +27. The 5'-boundary of the minimal core promoter capable of transcription initiation, however, was found to lie between -38 and -26. The 3'-deletion extending to -2 and -5 still allowed some transcription, suggesting that the positioning of Pol I is directed by upstream sequences. The results of in vitro analysis of linker scanning mutants (LSMs) combined with the deletion analysis showed that the promoter consists of three domains: two essential core domains (I: -28 to +8 and II: -76 to -51) and a transcription modulating upstream domain (III: -146 to -91). These results are in general agreement with those obtained in vivo (1). Using a template competition assay we also analyzed these mutant promoters for their ability to form a stable preinitiation complex. We found that the ability of 5'-deletion mutants to sequester an essential factor(s) correlates with their transcriptional activity. In contrast, several 3'-deletions and some LSMs in domain I and II decrease transcription activity greatly without significantly decreasing competition ability. The results indicate that the stimulatory function of domain III is achieved through its interaction with an essential transcription factor(s), although the other domains also participate in this interaction, perhaps directly or through another protein factor.