Transcription of nearly all yeast RNA Polymerase II-transcribed genes is dependent on transcription factor TFIID

Previous studies suggested that expression of most yeast mRNAs is dominated by either transcription factor TFIID or SAGA. We reexamined this longstanding problem by rapid depletion of TFIID subunits and measurement of changes in nascent transcription. We find that transcription of nearly all mRNAs is strongly dependent on TFIID function. Degron-dependent depletion of Tafs 1,2,7,11, and 13 showed similar transcription decreases for genes in the Taf1-depleted, Taf1-enriched, TATA-containing and TATA-less gene classes. The magnitude of TFIID-dependence varies with growth conditions, although this variation is similar at all gene classes. Many studies have suggested differences in gene regulatory mechanisms between TATA and TATA-less genes and these differences have been attributed in part to differential dependence on SAGA or TFIID. Our work indicates that TFIID contributes significantly to expression of nearly all yeast mRNAs and that differences in regulation between these two gene classes is due to other properties. Overall design: We used the auxin-inducible degron system to rapidly deplete selected TFIID subunits and Med14 subunit of Mediator. We then monitored genome-wide nascent transcription using native Pol II ChIP to analyze the position of Pol II elongation complexes before and after auxin-induced depletion of selected TFIID subunits and Med14 subunit of Mediator.