High-resolution binding data of TFIID and cofactors show promoter-specific differences

Abstract TFIID is instrumental in recognizing promoter sequences and initiating transcription, yet a cohesive understanding of how this complex engages and functions at different promoter types in vivo is still lacking. Here, we employed ChIP-nexus to capture high-resolution binding footprints of all Drosophila TFIID subunits across the genome. These footprints reveal TFIID sub-modules whose DNA contacts agree with cryo-EM structures and point to new structural details. At different promoter types, the footprints of the TAFs are very similar, suggestive of the same engaged TFIID conformation. In contrast, the binding profile of TBP is promoter-specific, enabling us to identify TATA, DPR, and TCT/housekeeping promoters de novo, along with their underlying core promoter elements. Notably, TATA promoters display specific TBP and NC2 binding footprints and reduced TAF occupancy, consistent with a fraction of transcripts being initiated in a TAF-independent manner at these promoters in vivo. Together, our results provide a comprehensive resource for linking structural and biochemical results to in vivo data and offer a potential explanation for the increased burst size observed at TATA promoters.