Human TFIID binds to core promoter DNA in a reorganized structural state

Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA.
Cell (Impact Factor: 32.24). 01/2013; 152(1-2):120-131. DOI: 10.1016/j.cell.2012.12.005
Source: PubMed


A mechanistic description of metazoan transcription is essential for understanding the molecular processes that govern cellular decisions. To provide structural insights into the DNA recognition step of transcription initiation, we used single-particle electron microscopy (EM) to visualize human TFIID with promoter DNA. This analysis revealed that TFIID coexists in two predominant and distinct structural states that differ by a 100 Å translocation of TFIID's lobe A. The transition between these structural states is modulated by TFIIA, as the presence of TFIIA and promoter DNA facilitates the formation of a rearranged state of TFIID that enables promoter recognition and binding. DNA labeling and footprinting, together with cryo-EM studies, were used to map the locations of TATA, Initiator (Inr), motif ten element (MTE), and downstream core promoter element (DPE) promoter motifs within the TFIID-TFIIA-DNA structure. The existence of two structurally and functionally distinct forms of TFIID suggests that the different conformers may serve as specific targets for the action of regulatory factors.

Download full-text


Available from: Patricia Grob,
  • Source
    • "There is the added challenge that these complexes often adopt alternative configurations and conformations on promoter templates. However, recent improvements in high-resolution EM methods have led to some significant advances, including the structural determinations of the human TFIID complex and a nearly complete PIC (Cianfrocco et al., 2013; He et al., 2013; Liu et al., 2009; Murakami et al., 2013). EM structures of human TFIID bound to DNA revealed that this core component of the PIC induces even more dramatic turns of the promoter template than the binding of TBP to TATA DNA (Figure 3A). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Comparative genome analyses reveal that organismal complexity scales not with gene number but with gene regulation. Recent efforts indicate that the human genome likely contains hundreds of thousands of enhancers, with a typical gene embedded in a milieu of tens of enhancers. Proliferation of cis-regulatory DNAs is accompanied by increased complexity and functional diversification of transcriptional machineries recognizing distal enhancers and core promoters and by the high-order spatial organization of genetic elements. We review progress in unraveling one of the outstanding mysteries of modern biology: the dynamic communication of remote enhancers with target promoters in the specification of cellular identity.
    Cell 03/2014; 157(1):13-25. DOI:10.1016/j.cell.2014.02.009 · 32.24 Impact Factor
  • Source
    • "A major component lacking from the model in Figure 10 is the TFIID complex. Given the large size of TFIID and its welldocumented structural dynamics (Cianfrocco et al., 2013; Grob et al., 2006), several possibilities can be envisioned for how TFIID might assemble. Although the PIC model shown in Figure 10 is speculative and will likely be revised once additional data with larger PIC assemblies are obtained, it illustrates several important points. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Abstract The Mediator complex is a multi-subunit assembly that appears to be required for regulating expression of most RNA polymerase II (pol II) transcripts, which include protein-coding and most non-coding RNA genes. Mediator and pol II function within the pre-initiation complex (PIC), which consists of Mediator, pol II, TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH and is approximately 4.0 MDa in size. Mediator serves as a central scaffold within the PIC and helps regulate pol II activity in ways that remain poorly understood. Mediator is also generally targeted by sequence-specific, DNA-binding transcription factors (TFs) that work to control gene expression programs in response to developmental or environmental cues. At a basic level, Mediator functions by relaying signals from TFs directly to the pol II enzyme, thereby facilitating TF-dependent regulation of gene expression. Thus, Mediator is essential for converting biological inputs (communicated by TFs) to physiological responses (via changes in gene expression). In this review, we summarize an expansive body of research on the Mediator complex, with an emphasis on yeast and mammalian complexes. We focus on the basics that underlie Mediator function, such as its structure and subunit composition, and describe its broad regulatory influence on gene expression, ranging from chromatin architecture to transcription initiation and elongation, to mRNA processing. We also describe factors that influence Mediator structure and activity, including TFs, non-coding RNAs and the CDK8 module.
    Critical Reviews in Biochemistry and Molecular Biology 10/2013; 48(6). DOI:10.3109/10409238.2013.840259 · 7.71 Impact Factor
  • Source
    • "Structural heterogeneity has been observed in TFIID preparations isolated from human cells and this was linked to a sub-stoichiometric TAF2 presence [8]. Additionally, the binding of TFIID to DNA induces a structural rearrangement within the complex [9]. The mechanism for this remains to be elucidated and it might be influenced by changes in TFIID composition. "
    [Show abstract] [Hide abstract]
    ABSTRACT: 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.
    PLoS ONE 09/2013; 8(9):e73495. DOI:10.1371/journal.pone.0073495 · 3.23 Impact Factor
Show more