RNA polymerase II-TFIIE-TFIIH interface functions in transcription start site selection in Saccharomyces cerevisiae

During initiation in Saccharomyces cerevisiae, Pol II, and the general transcription factors (GTFs) assemble upstream of transcription start sites to form the pre-initiation complex (PIC). The PIC selects transcription start sites (TSSs) by unidirectional scanning downstream from the site of PIC assembly. Studies indicate that during initiation, the TFIIH component Tfb3 links TFIIH to the rest of the PIC via interactions with Pol II and TFIIE. Here, we report the identification of tfb3 and tfa1 alleles conferring transcription-related phenotypes in vivo by genetic screens. These phenotypes are consistent with altered initiation. These alleles, many of which have residues conserved from budding yeast to human, show TSS shifts at the genetic reporters and genome-wide assay (STRIPE-Seq and TSS-sequencing). Our phenotypic and genomic data suggest that these alleles at the interface play a critical role in TSS selection during transcription initiation.