A sequence pattern that occurs at the transcription initiation region of yeast RNA polymerase II promoters

Saccharomyces cerevisiae mRNA 5'-ends map at a variable distance from the TATA element. The mechanism for the choice of the transcription Initiation Region (IR) over other neighbouring sequences is not clearly understood. Sequences on the coding strand flanking the IR of 95 yeast RNA polymerase II promoters have been compared. They indicate the following pattern: statistically, a preponderance of T residues beginning as far as 30 nucleotides upstream and ending approximately 10 nucleotides upstream of the IR, and a preponderance of A residues from approximately 8 nucleotides upstream of the transcription initiation-site onward. The switch in base composition noted above thus occurs over a short region that is centered typically -9 nucleotides with respect to the major transcription start-site. We call this overall sequence pattern the locator. It is more evident among strong promoters than weak ones, suggesting a role in transcription initiation. The promoter of the TCM1 gene (coding for ribosomal protein L3) has a typical locator in the region of its IR. In an attempt to confirm the role of this sequence motif in defining the IR, deletions were introduced between the TATA element and the IR of the TCM1 gene. In most deletions, the new transcription start-sites are found within a recognizable locator, supporting the suggestion that this sequence pattern is important in defining the IR. These data appear to indicate that in yeast the IR is defined by a pattern of base composition situated at a suitable distance from the TATA element.