Genome-wide relationships between TAF1 and histone acetyltransferases in S. cerevisiae

Evidence suggests that the TAF1 subunit of TFIID is a histone acetyltransferase (HAT) that is functionally redundant with the Gcn5 HAT of the SAGA and ADA complexes. Here we test a number of predictions of this hypothesis by examining the in vivo histone acetylation targets of TAF1 and Gcn5, and re-examining the basis for the reported genome-wide functional redundancy between TAF1 and Gcn5. Our findings do not support a number of basic tenets of the hypothesis, thus bringing into question the physiological presence of any TAF1 HAT function in yeast. We have also conducted genome-wide expression profiles of numerous other HATs (Elp3, Hat1, Hpa2, Sas3) in an effort identify potential functional redundancy between TAF1 and other HATs, and find none. Further investigation of TAF1 and the Esa1 HAT re-affirm a link between histone H4 acetylation by Esa1, and TFIID binding via interactions with acetylated histone H4-binding protein Bdf1. Keywords: genetic modification Experiment contains 38 total hybridizations. Yeast cDNA dual channel (Cy3/Cy5) cohybridization. All experiments performed in duplicate (dye swap). Dye swap data was mode normalized using "R" software package and then corrected by B. subtilis spiking controls (added to each culture based on OD600 units). Platform GPL1220: non-commercial nucleotide arrays. PCR amplified yeast (Saccharomyces cerevisiae) genomic DNA chip with ResGen Primer Pairs. Amplification as described at http://cmgm.stanford.edu/pbrown/protocols/2_DNA.html. Printed on aminosaline glass slides by the Penn State University Microarray facility