A comparison of RNA polymerase III genes with external promoters

Eukaryotic gene expression is regulated mostly at the level of transcription. Gene promoters are essential components for transcriptional regulation. There are core promoter sequences that specify the accurate initiation site of transcription and enhancers that stimulate the level of transcription. For eukaryotes there are three RNA polymerases that share the role of transcribing the major classes of genes in the nucleus, each with their own types of promoters. RNA polymerase III transcribes genes containing three subclasses of promoters, with the third subclass composed of upstream promoter elements similar to the RNA polymerase II promoters. Characterization of promoters of this subclass, namely the human U6 small nuclear RNA (snRNA) genes and the Tetrahymena thermophila telomerase RNA subunit gene was undertaken. It was previously thought that there was only one full-length “true” human U6 snRNA gene. We have now identified eight additional full-length U6 snRNA genes and/or pseudogenes containing distinct 5′ flanking regions. Four of the variants contained most of the known human U6 promoter elements and were to found to be transcriptionally active both in vivo and in vitro although to varying extents. The other four variants did not contain any known promoter elements and were found to be pseudogenes and not transcriptionally active in vivo or in vitro. The other promoter that was characterized, the Tetrahymena thermophila telomerase RNA subunit gene promoter, was found to contain promoter elements similar to the U6 snRNA gene promoter. This promoter contains an essential TATA and proximal sequence element (PSE). A protein that binds to the PSE was identified and partially characterized. This PSE-binding protein recognizes both the Tetrahymena telomerase RNA subunit gene promoter as well as the Tetrahymena U snRNA gene promoters. These promoters from two diverse organisms are a bridge between the RNA polymerase 11 and III transcribed genes and expanding information about them will lead to a better understanding of transcriptional control mechanisms.