Coactivator SAGA plays a crucial role in TBP recruitment for the Gcn4 transcriptome via subunits Spt3/Spt8
Coactivator complexes TFIID and SAGA recruit TATA-binding protein (TBP), while SAGA also enhances transcription by histone acetylation via the HAT Gcn5. It was proposed that most yeast genes depend exclusively on TFIID, with only ~10% requiring cumulative contributions by SAGA and TFIID for efficient transcription. It was further suggested that genes induced by Gcn4, transcriptional activator of amino acid biosynthetic genes induced by amino acid starvation, depend on the HAT, but not TBP-recruitment function of SAGA. At odds with this model, ChIP-sequencing of TBP and Pol II subunit Rpb1 revealed that deleting SPT3 or SPT8, but not GCN5, reduced TBP binding at most Gcn4 target genes, whereas deleting GCN5 selectively impaired promoter histone eviction; and all three SAGA mutations reduced transcription comparably. Nuclear depletion of TFIID subunit Taf1 generally reduced TBP recruitment at these and most other SAGA-dependent genes only in cells lacking Spt3 or Spt8. We conclude that SAGA is crucial for TBP recruitment via Spt3/Spt8, beyond its role in histone acetylation, whereas TFIID plays an ancillary role for the Gcn4 transcriptome in amino acid-starved cells. Overall design: Formaldehyde-fixed and sonicated DNA fragments were immunopurified and subjected to paired-end sequencing.