TFIID and SAGA functions probed by genome-wide synthetic genetic array (SGA) analysis using a Saccharomyces cerevisiae taf9-ts allele

# These authors contributed equally to this work. ABSTRACT TAF9 is a TATA binding protein associated factor (TAF) conserved from yeast to humans, and shared by two transcription coactivator complexes, TFIID and SAGA. The essentiality of the TAFs has made it difficult to ascertain their roles in TFIID and SAGA function. Here, we performed a genomic synthetic genetic array analysis using a temperature sensitive allele of TAF9 as a query. Results from this experiment showed that TAF9 interacts genetically with: 1) genes for multiple transcription factor complexes involving predominantly Mediator, chromatin modification/remodeling complexes, and regulators of transcription elongation; 2) virtually all non-essential genes encoding subunits of the SWR-C chromatin-remodeling complex, and both TAF9 and SWR-C are required for expressing the essential housekeeping gene RPS5; 3) key genes for cell cycle control at the G1/S transition, as well as genes involved in cell polarity, cell integrity, and protein synthesis, suggesting a link between TAF9 function and cell growth control. We also showed that disruption of SAGA by deletion of SPT20 alters histone-DNA contacts and phosphorylated forms of RNA polymerase II at coding sequences. Our results raise the possibility of an unappreciated role for TAF9 in transcription elongation, perhaps in the context of SAGA, and provide further support for TAF9 involvement in cell cycle progression and growth control.