Transcription initiation mediated by initiator binding protein in Saccharomyces cerevisiae

Many instances of the initiator element in the core promoter of protein-coding genes have been reported in mammalian cells and their viruses, but only one has been reported in the yeast Saccharomyces cerevisiae at the GAL80 gene. The initiator element of GAL80 directs transcription by itself and interacts with a nuclear protein designated yeast initiator binding factor (yIF). Here we show that yIF in a partially purified sample binds the sequence from -18 to +10 of GAL80. By employing a selected and amplified binding procedure, we have determined the preferred sequence for yIF binding to be -2 CACTN +3 (N indicates any nucleotide). Binding affinity of selected sequences to yIF correlated with their initiator-directed transcription in vivo, suggesting that the yIF-initiator interaction mediates transcription from the initiator in yeast. We also suggest that sequences flanking the preferred sequence affect both yIF binding and initiator activity.