Multivalent engagement of TFIID to nucleosomes.

The process of eukaryotic transcription initiation involves the assembly of basal transcription factor complexes on the gene promoter. The recruitment of TFIID is an early and important step in this process. Gene promoters contain distinct DNA sequence elements and are marked by the presence of post-translationally modified nucleosomes. The contributions of these individual features for TFIID recruitment remain to be elucidated. Here, we use immobilized reconstituted promoter nucleosomes, conventional biochemistry and quantitative mass spectrometry to investigate the influence of distinct histone modifications and functional DNA-elements on the binding of TFIID. Our data reveal synergistic effects of H3K4me3, H3K14ac and a TATA box sequence on TFIID binding in vitro. Stoichiometry analyses of affinity purified human TFIID identified the presence of a stable dimeric core. Several peripheral TAFs, including those interacting with distinct promoter features, are substoichiometric yet present in substantial amounts. Finally, we find that the TAF3 subunit of TFIID binds to poised promoters in an H3K4me3-dependent manner. Moreover, the PHD-finger of TAF3 is important for rapid induction of target genes. Thus, fine-tuning of TFIID engagement on promoters is driven by synergistic contacts with both DNA-elements and histone modifications, eventually resulting in a high affinity interaction and activation of transcription.

Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II.

The precise, sequence-specific regulation of RNA synthesis is the primary mechanism underlying differential gene expression. This general statement applies to both prokaryotic and eukaryotic organisms, as well as to their viral pathogens. Thus, it is not surprising that genomes use a substantial portion of their protein-coding content to regulate the process of RNA synthesis. Transcriptional regulation in bacterial systems is particularly well understood. In this essay, we build on this knowledge and propose two opposing models to describe promoter opening and transcription initiation in the eukaryotic RNA polymerase II system. Promoter opening in the "twisting by cranking" model is based on changes in the trajectory of DNA. In contrast, invasion of single-stranded DNA-binding proteins between the DNA strands drives the reaction in the "peeling by binding" model.