The seemingly identical 7SK and U6 core promoters depend on different transcription factor complexes.

Fractions obtained from HeLa cell extracts were used to study RNA polymerase III-catalyzed transcription from the human 7SK and mouse U6 RNA promoters in vitro. Although both genes depend on two almost identical core promoter elements (TATA box and PSE), different fractions were required. The 7SK promoter revealed full activity with the phosphocellulose B fraction alone. In contrast, efficient transcription from the U6 promoter depended on the additional presence of the C or D fraction. The analysis of the b1 and b2 subfractions (obtained by DEAE-Sephadex chromatography) revealed that for both promoters the b1 and the phosphocellulose D fraction were mutually interchangeable. However, while both fractions were fully equivalent for the 7SK promoter, the U6 promoter revealed an additional requirement for the C fraction in the presence of the b1 fraction. Since the b1 and the D fractions enclose two different complexes of the TATA-binding protein (TBP), B-TFIID and D-TFIID, our results indicate that functionally these two complexes are responsible for the observed differences in transcription of the 7SK and U6 genes.