Abstract: Two of the major histone acetyltransferases in S. cerevisiae are NuA4 and SAGA, which acetylate histones H4 and H3, respectively. Acetylated H3 and H4 tails have been implicated in binding bromodomain proteins, including Bdf1. Bdf1 interacts with general transcription factor TFIID, which might promote pre-initiation complex (or PIC) assembly. Bdf1 also interacts with the SWR complex (SWR-C). SWR-C is responsible for deposition of the histone H2A variant H2A.Z. Placement of interactions into a connected pathway of PIC assembly as not been fully established. Moreover, it is not known how widespread and how variable such a pathway might be on a genomic scale. Here we provide genomic evidence in S. cerevisiae that PIC assembly (TFIID occupancy) and chromatin remodeling (SWR-C and H2A.Z occupancy) are linked in large part to NuA4-directed H4 acetylation and subsequent Bdf1 binding, rather than through SAGA-directed H3 acetylation. Bdf1 and its homolog Bdf2 tend to have distinct locations in the genome. However, deletion of BDF1 leads to accumulation of Bdf2 at Bdf1-vacated sites. Thus, while Bdf1 and Bdf2 are at least partially redundant in function, their functions in the genome are geographically distinct.