Zooming in on Transcription Preinitiation

Abstract

Class II gene transcription commences with the assembly of the Preinitiation Complex (PIC) from a plethora of proteins and protein assemblies in the nucleus, including the General Transcription Factors (GTFs), RNA polymerase II (RNA pol II), co-activators, co-repressors, and more. TFIID, a megadalton-sized multiprotein complex comprising 20 subunits, is among the first GTFs to bind the core promoter. TFIID assists in nucleating PIC formation, completed by binding of further factors in a highly regulated stepwise fashion. Recent results indicate that TFIID itself is built from distinct preformed submodules, which reside in the nucleus but also in the cytosol of cells. Here, we highlight recent insights in transcription factor assembly and the regulation of transcription preinitiation.

Keywords: RNA polymerase II; general transcription factor TFIID; multiprotein complex; preinitiation complex; transcription initiation.

Graphical abstract

Fig. 1

Transcription PIC. Class II gene transcription is brought about by (in humans) over a hundred polypeptides assembling on the core promoter of protein-encoding genes, which then give rise to messenger RNA. A PIC on a core promoter is shown in a schematic representation (adapted from Ref. [5]). PIC contains, in addition to promoter DNA, the GTFs TFIIA, B, D, E, F, and H, and RNA Pol II. PIC assembly is thought to occur in a highly regulated, stepwise fashion (top). TFIID is among the first GTFs to bind the core promoter via its TBP subunit. Nucleosomes at transcription start sites contribute to PIC assembly, mediated by signaling through epigenetic marks on histone tails. The Mediator (not shown) is a further central multiprotein complex identified as a global transcriptional regulator. TATA, TATA-box DNA; BRE^u, B recognition element upstream; BRE^d, B recognition element downstream; Inr, Initiator; DPE, Down-stream promoter element.

Fig. 2

Mediator Core–ITC Architecture. The structure of a Mediator core bound to an initially transcribing RNA pol II-containing complex (EMD-2786; PDB ID: 4V1O) is shown in two views related by a 180° rotation along the vertical axis (arrow). TBP (green), promoter DNA (yellow and green), TFIIB (blue), TFIIF (purple), and the mediator Head module are depicted in a cartoon representation based on X-ray crystal structure coordinates. RNA Pol II is colored in gray. Mediator Middle Module (Knob, Hook) is colored in orange. The structure was determined by cryo-EM combined with CLMS and by fitting of available atomic coordinates (adapted from Ref. [24]).

Fig. 3

Human GTF TFIID. TFIID is a large megadalton-sized multiprotein complex comprising about 20 subunits made up of 14 different polypeptides. The constituent proteins of TFIID, TBP and the TAFs, are shown in a schematic representation depicted as bars (inset, left). Structured domains are marked and annotated. The presumed stoichiometry of TAFs and TBP in the TFIID holo-complex is given (far left, gray underlaid). TAF10 (in italics) makes histone fold pair separately with both TAF3 and TAF8. TAFs present in a physiological TFIID core complex extracted from eukaryotic nuclei are labeled in bold. The architecture of TFIID core complex (EMD-2230) determined by cryo-EM is shown (bottom left) in two views related by a 90° rotation (arrows) . The holo–TFIID complex is characterized by remarkable structural plasticity. Two conformations, based on cryo-EM data (EMD-2284 and EMD-2287), are shown on the right, a canonical form (top) and a more recently observed rearranged form (bottom). In the rearranged conformation, lobe A (colored in red) migrates from one extreme end of the TFIID complex (attached to lobe C) all the way to the other extremity (attached to lobe B) .

Fig. 4

Preformed TFIID Submodule in Cytoplasm. Recently, a stable TFIID subcomplex consisting of TAF2, TAF8, and TAF10 has been discovered, surprisingly residing in the cytoplasm of cells. TAF2, TA8, and TAF10 are shown in a schematic representation (top), depicted as bars. TAF2 is characterized by an extended aminopeptidase-like fold. TAF8 and TAF10 contain HFDs. The TAF8 domain mediating interaction with TAF2 has been identified (marked as 2ID). TAF8 and TAF10 form an HFD pair in the TAF2–8–10 complex. TAF8 contains a nuclear localization signal (black box), and a stable putative nuclear import complex comprising one copy each of TAF2, TAF8, TAF10, and Importin-α could be purified to homogeneity (bottom left). A model of this NIP is shown (inset), based on crystal structures (TAF8–TAF10; TAF8–Imp) (PDB IDs: 4WV4 and 4WV6) and a model of TAF2 threaded on highly homologous human aminopeptides ERAP (adapted from Ref. [45]).

Fig. 5

TFIID Domain Structure Gallery. A range of structure of TFIID domains and domain components has been determined at near atomic resolution, mostly by X-ray crystallography. Structures shown here include structures of HFD pairs (top row): Drosophila TAF6–TAF9 (PDB ID: 1TAF) , human TAF8–TAF10 (PDB ID: 4WV4) , human TAF11–TAF13 (PDB ID: 1BH8) , and human TAF4–TAF12 (PDB ID: 1H3O) . Crystal structures of isolated single domains of a variety of TAFs have been solved: human TAF5_NTD (PDB ID: 2NXP) , human TAF1_DBD (double bromodomain) (PDB ID: 1EQF) , the A. locustae TAF6_HEAT repeat (PDB ID: 4ATG) , human TAF4_TAFH (PDB ID: 2P6V) , and an NMR-based structure of mouse TAF3_PHD (PDB ID: 2K16) . The conserved core of TBP has been studied intensively, and a selection of TBP-containing structures is shown: human TBP in complex with TATA-box DNA (PDB ID: 1CDW) , a yeast TBP dimer (PDB ID: 1TBP) , a yeast TBP–TAF1_TAND complex (PDB ID: 4B0A) , human TBP/TFIIA/DNA complex (PDB ID: 1NVP) . More recently, crystal structures of pairwise interactions within TFIID other than HFDs have been obtained: a yeast TAF1–TAF7 complex (left) (PDB ID: 4OY2) and a partial human TAF1-TAF7 counterpart (right) (PDB ID: 4RGW) were crystallized and their structure determined .

Fig. 6

Brf2–TBP–DNA Complex. The crystal structure of Brf2 bound to TBP (green) and promoter DNA (orange) is shown (PDB ID: 4ROC). Brf2 is shown in a schematic representation, depicted as a bar (top). Linker, cyclin domains, and CTD are indicated. The Brf2 CTD reaches over to interact with the convex surface of TBP, mediated by a molecular pin and an anchor domain (adapted from Ref. [67]).