Research Article

Structural insights into preinitiation complex assembly on core promoters

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Science  30 Apr 2021:
Vol. 372, Issue 6541, eaba8490
DOI: 10.1126/science.aba8490

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Assembling for transcription initiation

Eukaryotic transcription initiation by RNA polymerase II (Pol II) requires the assembly of a preinitiation complex (PIC) on core promoters. The binding of TATA box–binding protein (TBP) to the TATA box promoter has been thought to be a general rule in PIC assembly and transcription initiation. However, most coding genes lack a TATA box, and nearly all Pol II–mediated gene transcription requires the TBP-containing multisubunit complex transcription factor IID (TFIID). Chen et al. determined the structures of human TFIID-based PIC in sequential assembly states and revealed that TFIID supports distinct PIC assembly on TATA-containing and TATA-lacking promoters. The finding resolves the long-standing mystery of how one set of general transcription machinery initiates transcription on diverse promoters.

Science, this issue p. eaba8490

Structured Abstract

INTRODUCTION

RNA polymerase II (Pol II)–mediated transcription initiation requires assembly of a preinitiation complex (PIC), during which the 14-subunit transcription factor IID (TFIID) recognizes core promoters and recruits TFIIA, TFIIB, TFIIE, TFIIF, TFIIH, and Pol II to sequentially assemble core PIC (cPIC), intermediate PIC (mPIC), and holo PIC (hPIC). The textbook model of transcription initiation starts with binding of TBP (TATA box–binding protein, a TFIID subunit) to TATA box. However, up to 85% of coding genes lack consensus TATA box, and the TFIID complex is required for almost all Pol II–mediated gene transcription. Despite extensive structural studies of TBP-based PIC on TATA box promoters, it remains elusive how TFIID supports PIC assembly on different promoters.

RATIONALE

We reconstituted and determined cryo–electron microcopy structures of the human TFIID-based PIC. Stepwise PIC assembly was characterized by 25 complex structures in different compositional and conformational states on 13 different (natural, composite, and mutant) promoters. Structures of Pol II, TFIID modules, and TBP-promoter at near-atomic resolution permit detailed structural analyses.

RESULTS

Structures in distinct conformations reveal a shared TFIID-binding pattern and loading of TBP to TATA and TATA-less promoters. Unexpectedly, TBP similarly bends TATA box and TATA-less promoters in PIC. PIC assembly on different promoters diverges into two tracks at cPIC and converges at hPIC. On track I, cPIC, mPIC, and hPIC on TATA-DBE promoters adopt the Park, Neutral, and Drive conformations, respectively, indicating stepwise promoter deposition to Pol II accompanied by extensive modular reorganization. On track II, cPIC, mPIC, and hPIC on TATA-only and TATA-less promoters adopt the Drive conformation, indicating direct promoter deposition. The differences result from distinct promoter compositions, which lead to “matched” versus “repositioned” modular separation on promoters and result in distinct PIC architectures and promoter trajectories. In hPIC, TFIID stabilizes PIC organization and supports loading of cyclin-dependent kinase 7 (CDK7) onto Pol II and CDK7-mediated C-terminal domain (CTD) phosphorylation.

CONCLUSION

Our study resolves the long-standing controversy between the lack of TATA box in most core promoters and the necessity of the TFIID complex (but not TBP alone) in transcription. TFIID recognizes promoters and supports TBP-induced promoter bending and two-track PIC assembly on highly diversified core promoters. The stepwise promoter deposition may serve as a checkpoint to prevent promiscuous initiation before PIC is fully assembled, and the hPIC offers a shared starting point for transcription initiation independent of promoter type. Structural visualization of PIC assembly provides a framework for further studies of transcription initiation in the context of transcription factors, coactivators, and epigenetic regulators.

Schematic model of PIC assembly.

Proposed working model of TFIID-supported promoter recognition (inner section) and two-track PIC assembly on different promoters (outer section). P, N, and D denote the Park, Neutral, and Drive conformations, respectively. Right panels (with dashed outlines): Comparison of promoter conformations in cPIC (red), mPIC (yellow), and hPIC (green). Lower panel: The matched and repositioned modular separation on promoters during cPIC assembly. Structures are derived from this study, and representative core promoters are indicated. HMG, high-mobility group; DBE, TFIID-binding element; CAK, CDK-activating kinase.

Abstract

Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)–mediated eukaryotic transcription. We determined the structures of human TFIID–based PIC in three stepwise assembly states and revealed two-track PIC assembly: stepwise promoter deposition to Pol II and extensive modular reorganization on track I (on TATA–TFIID-binding element promoters) versus direct promoter deposition on track II (on TATA-only and TATA-less promoters). The two tracks converge at an ~50-subunit holo PIC in identical conformation, whereby TFIID stabilizes PIC organization and supports loading of cyclin-dependent kinase (CDK)–activating kinase (CAK) onto Pol II and CAK-mediated phosphorylation of the Pol II carboxyl-terminal domain. Unexpectedly, TBP of TFIID similarly bends TATA box and TATA-less promoters in PIC. Our study provides structural visualization of stepwise PIC assembly on highly diversified promoters.

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