Genetic dissection of NuA4-directed chromatin transactions throughout the S. cerevisiae genome

Acetylation of histone tails has long been associated with gene activation. Exactly how acetylation regulates gene expression is not fully known. Acetylation events at specific sites or collections of sites on histones elicit distinct outcomes. Here we examine the downstream consequences of histone acetylation by the histone H4 acetyltransferase NuA4 on a genomic scale. Evidence is presented that Bdf1, which is known to bind to acetylated lysine H4 tails in vitro, binds to nucleosomes in vivo and that this binding is dependent upon Esa1, the catalytic subunit of NuA4. Loss of NuA4 results in a coordinate depletion of Bdf1, the transcription complex assembly factor TFIID, and the H2A.Z assembly complex SWR-C at highly acetylated promoter regions. This finding is consistent with known interactions between Bdf1 and TFIID and SWR-C. Loss of Bdf1 results in little or no depletion of TFIID or SWR-C at these promoter regions, possibly due to substitution by the Bdf1 paralog Bdf2. Consistent with this possibility, loss of Bdf1 results in accumulation of Bdf2 at sites normally bound by Bdf1. Together, the findings presented here strengthen the proposed cascade of events whereby nucleosome H4 acetylation by NuA4 at promoters target Bdf1, which then recruits TFIID and SWR-C to assemble the transcription machinery. Keywords: chIP-chip, histone acetylation, transcription factor recruitment Experiment contains 22 total hybridizations. Yeast enriched chIP DNA dual channel (Cy3/Cy5) cohybridization. All experiments performed in duplicate (dye swap). Dye swap data was normalized by centering to the average log2 ratio of the non-promoter regions. Platform GPL1924: non-commercial nucleotide arrays. PCR amplified yeast (Saccharomyces cerevisiae) genomic DNA chip. Printed on aminosaline glass slides by the Penn State University Microarray facility