Redundant roles for the TFIID and SAGA complexes in global transcription

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Abstract
The transcription factors TFIID and SAGA are multi-subunit complexes involved in transcription by RNA polymerase II1,2. TFIID and SAGA contain common TATA-binding protein (TBP)-associated factor (TAFII) subunits and each complex contains a subunit with histone acetyltransferase activity3. These observations have raised questions about whether the functions of the two complexes in vivo are unique or overlapping. Here we use genome-wide expression analysis to investigate how expression of the yeast genome depends on both shared and unique subunits of these two complexes. We find that expression of most genes requires one or more of the common TAFII subunits, indicating that the functions of TFIID and SAGA are widely required for gene expression. Among the subunits shared by TFIID and SAGA are three histone-like TAFIIs, which have been proposed to form a sub-complex and mediate a common function in global transcription. Unexpectedly, we find that the histone-like TAFIIs have distinct roles in expression of the yeast genome. Most importantly, we show that the histone acetylase components of TFIID and SAGA (TAFII145 and Gcn5) are functionally redundant, indicating that expression of a large fraction of yeast genes can be regulated through the action of either complex.