Regulatory interplay between TFIID's conformational transitions and its modular interaction with core promoter DNA

Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factor TFIID

Previous studies suggested that expression of most yeast mRNAs is dominated by either transcription factor TFIID or SAGA. We re-examined the role of TFIID by rapid depletion of S. cerevisiae TFIID subunits and measurement of changes in nascent transcription. We find that transcription of nearly all mRNAs is strongly dependent on TFIID function. Degron-dependent depletion of Taf1, Taf2, Taf7, Taf11, and Taf13 showed similar transcription decreases for genes in the Taf1-depleted, Taf1-enriched, TATA-containing, and TATA-less gene classes. The magnitude of TFIID dependence varies with growth conditions, although this variation is similar genome-wide. Many studies have suggested differences in gene-regulatory mechanisms between TATA and TATA-less genes, and these differences have been attributed in part to differential dependence on SAGA or TFIID. Our work indicates that TFIID participates in expression of nearly all yeast mRNAs and that differences in regulation between these two gene categories is due to other properties.

Structural Insights into the Eukaryotic Transcription Initiation Machinery

Eukaryotic gene transcription requires the assembly at the promoter of a large preinitiation complex (PIC) that includes RNA polymerase II (Pol II) and the general transcription factors TFIID, TFIIA, TFIIB, TFIIF, TFIIE, and TFIIH. The size and complexity of Pol II, TFIID, and TFIIH have precluded their reconstitution from heterologous systems, and purification relies on scarce endogenous sources. Together with their conformational flexibility and the transient nature of their interactions, these limitations had precluded structural characterization of the PIC. In the last few years, however, progress in cryo-electron microscopy (cryo-EM) has made possible the visualization, at increasingly better resolution, of large PIC assemblies in different functional states. These structures can now be interpreted in near-atomic detail and provide an exciting structural framework for past and future functional studies, giving us unique mechanistic insight into the complex process of transcription initiation.

Structural dynamics and DNA interaction of human TFIID

TFIID is a large protein complex required for the recognition and binding of eukaryotic gene core promoter sequences and for the recruitment of the rest of the general transcription factors involved in initiation of eukaryotic protein gene transcription. Cryo-electron microscopy studies have demonstrated the conformational complexity of human TFIID, where one-third of the mass of the complex can shift its position by well over 100 Å. This conformational plasticity appears to be linked to the capacity of TFIID to bind DNA, and suggests how it would allow both the recognition of different core promoter elements and the tuning of its binding affinity by regulatory factors.

Cryo-EM in the study of challenging systems: the human transcription pre-initiation complex

Single particle cryo-Electron Microscopy (cryo-EM) is a technique that allows the structural characterization of macromolecules without the need for crystallization. For certain type of samples that are ideally suited for cryo-EM studies it has been possible to reach high-resolution structures following relatively standard procedures. Other biological systems remain highly challenging, even for cryo-EM. Challenges may involve the scarcity of the sample, poor stability of the complexes, and most often, the intrinsic flexibility of biological molecules. Among these challenging samples are large eukaryotic transcription complexes, which suffer from all such shortcomings. Here we report how we have recently tried to overcome those challenges in order to improve our structural understanding of the human transcription pre-initiation complex assembly and the transcription initiation process. Parallel efforts have also been carried out for budding yeast transcription initiation complexes, allowing comparisons that establish both the overall conservation and the specific structural differences between the two systems.

The core promoter: At the heart of gene expression

The identities of different cells and tissues in multicellular organisms are determined by tightly controlled transcriptional programs that enable accurate gene expression. The mechanisms that regulate gene expression comprise diverse multiplayer molecular circuits of multiple dedicated components. The RNA polymerase II (Pol II) core promoter establishes the center of this spatiotemporally orchestrated molecular machine. Here, we discuss transcription initiation, diversity in core promoter composition, interactions of the basal transcription machinery with the core promoter, enhancer-promoter specificity, core promoter-preferential activation, enhancer RNAs, Pol II pausing, transcription termination, Pol II recycling and translation. We further discuss recent findings indicating that promoters and enhancers share similar features and may not substantially differ from each other, as previously assumed. Taken together, we review a broad spectrum of studies that highlight the importance of the core promoter and its pivotal role in the regulation of metazoan gene expression and suggest future research directions and challenges.

More pieces to the puzzle: recent structural insights into class II transcription initiation

Class II transcription initiation is a highly regulated process and requires the assembly of a pre-initiation complex (PIC) containing DNA template, RNA polymerase II (RNAPII), general transcription factors (GTFs) TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH and Mediator. RNAPII, TFIID, TFIIH and Mediator are large multiprotein complexes, each containing 10 and more subunits. Altogether, the PIC is made up of about 60 polypeptides with a combined molecular weight of close to 4MDa. Recent structural studies of key PIC components have significantly advanced our understanding of transcription initiation. TFIID was shown to bind promoter DNA in a reorganized state. The architecture of a core-TFIID complex was elucidated. Crystal structures of the TATA-binding protein (TBP) bound to TBP-associated factor 1 (TAF1), RNAPII-TFIIB complexes and the Mediator head module were solved. The overall architectures of large PIC assemblies from human and yeast have been determined by electron microscopy (EM). Here we review these latest structural insights into the architecture and assembly of the PIC, which reveal exciting new mechanistic details of transcription initiation.