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

## TL;DR

This study reveals how the TFIID complex interacts with different types of promoters in living cells, providing new insights into gene transcription initiation.

## Contribution

The paper introduces high-resolution in vivo binding data of TFIID subunits and cofactors, revealing promoter-specific interactions and structural details.

## Key findings

- TFIID subunits show similar footprints across all promoter types, suggesting consistent engagement.
- TBP binding is promoter-specific and helps identify distinct promoter classes like TATA, DPR, and TCT/housekeeping.
- NC2 is specific for TBP binding at TATA promoters, indicating dual initiation modes at these promoters.

## Abstract

TFIID is instrumental in recognizing promoter sequences and initiating transcription, yet a cohesive understanding of how this complex interacts with 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 suggest new structural details. At different promoter types, the footprints of the TAFs are very similar, suggesting the presence of engaged TFIID across all promoters. 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, our data point to NC2 being specific for TBP binding at the TATA box and suggest that TATA promoters show both TAF-dependent and TAF-independent initiation in vivo. These data suggest a model for the increased burst size observed at TATA promoters and provide a comprehensive resource for linking structural and biochemical results to in vivo data.