UC San Diego

The RNA polymerase II core promoter is a diverse and complex region of DNA that contains the transcription start site. Core promoter elements are conserved DNA sequences within the core promoter that direct transcription to the start site and function in the regulation of gene expression. Here I describe the TCT motif, a newly discovered core promoter element that encompasses the transcription start site and is conserved among the ribosomal protein genes. Mutational analysis of three ribosomal protein gene promoters, RpLP1, RpS12, and RpS15, demonstrates the importance of this DNA element. A severe down-regulation of transcription is seen when the wild-type sequence is mutated, with positions 3-5 (+3 to + 5 relative to the +1 transcription start site) being the most important. I also show that the TCT does not work synergistically with other previously characterized core promoter elements, and the RpLP1 promoter is not bound by Transcription Factor IID (TFIID). The TCT is a necessary core promoter element for the transcription of the ribosomal protein genes. Its inability to work synergistically with other known promoter elements, along with its inability to bind TFIID, may suggest a parallel mechanism of RNA polymerase II transcription for the ribosomal protein genes that is independent of the mechanism used for all previously studied genes