Genome-wide Organization of the Basal Transcription Factor TFIID

TFIID is a multi-subunit complex containing TBP and 13 TBP-associated factors (TAFs). It plays a key role in the initiation of transcription by recognizing promoter-specific sequence elements, leading to the assembly of the pre-initiation complex (PIC) machinery and the recruitment of the RNA-polymerase II. In vitro, TFIID uses different subunits to interact with such elements and changes its structural configuration when binding DNA. While motif composition is very diverse at endogenous promoters, whether all TFIID subunits are present across promoters or whether its binding organization changes in vivo with consequences for transcription is not understood. Here, we used ChIP-nexus, a technique that detects in vivo binding at base-pair resolution, to investigate the DNA-bound composition and organization of all 14 TFIID subunits in the Drosophila melanogaster genome. We found that the in vivo footprints of TFIID can be divided into three structurally distinguishable sub-modules whose binding is remarkably homogeneous across different promoter types. In contrast to the TAFs, the footprints for TBP were distinct for TATA, DPR, and housekeeping promoter types and revealed their underlying sequence elements. At most promoter types, TBP is found upstream and downstream of the start site dependent on the transcriptional state, but the amount and exact profile at each position differs between promoter types. We propose that TBP is first loaded downstream of the core promoter and then transferred upstream to assemble the transcription machinery, and that the time spent at each location depends on the promoter type and transcriptional activity. Taken together, our results suggest different rate-limiting states of TFIID recruitment between promoter types. We discuss the implications of this model for the transcription properties of each promoter