Eukaryotic Transcription Machinery

Eukaryotes transcribe their genomes with three nuclear DNA-dependent RNA polymerases, of which RNA polymerase II transcribes all protein-coding genes and many noncoding RNAs. Unlike the comparatively self-sufficient bacterial enzyme, eukaryotic polymerases require large assemblies of accessory factors to recognise promoters, assemble at the start site and proceed through chromatin.

Definition

RNA polymerase II is the eukaryotic DNA-dependent RNA polymerase that transcribes messenger RNA precursors and many noncoding RNAs; the eukaryotic transcription machinery is the polymerase together with the general transcription factors, Mediator and associated proteins that assemble and regulate transcription at a promoter.

Scope

The topic covers the eukaryotic RNA polymerases (with emphasis on RNA polymerase II), the general transcription factors and the preinitiation complex they form, the Mediator coactivator, and the regulated transitions of initiation, pausing and elongation. It is treated at a reference-educational level and not as clinical guidance.

Core questions

• How is the RNA polymerase II preinitiation complex assembled at a promoter?
• What roles do the general transcription factors and the Mediator complex play?
• How do promoter-proximal pausing and elongation control regulate Pol II transcription?

Key concepts

• RNA polymerases I, II and III
• General transcription factors (e.g. TFIID, TFIIB, TFIIE, TFIIF, TFIIH)
• Preinitiation complex
• Mediator complex
• C-terminal domain (CTD) of Pol II
• Promoter-proximal pausing
• Coupling of elongation to RNA processing

Mechanisms

RNA polymerase II is recruited to a promoter as part of a preinitiation complex assembled from the general transcription factors, which recognise core-promoter elements, position the polymerase, melt the DNA and allow synthesis to begin; the Mediator complex bridges gene-specific activators to this machinery. After initiation, Pol II frequently pauses just downstream of the start site and requires further factors to enter productive elongation, during which the phosphorylation state of the polymerase C-terminal domain coordinates capping, splicing and 3'-end processing of the transcript. The atomic structure of RNA polymerase II revealed the conserved cleft, clamp and active site that underlie these steps, building on the original discovery that eukaryotes deploy multiple specialised polymerases.

Clinical relevance

Components of the eukaryotic transcription machinery, including Mediator subunits and the kinases that control pausing and elongation, are implicated in cancer and developmental disorders and are studied as drug targets; the Pol II inhibitor α-amanitin is a classic experimental and toxicological agent. This entry describes these mechanisms at a reference level and is not a basis for treatment decisions.

History

The recognition that eukaryotes possess multiple RNA polymerases (Roeder and Rutter, 1969) opened the study of a dedicated, multi-component transcription apparatus. Subsequent reconstitution of the general transcription factors, discovery of the Mediator complex, and the high-resolution structure of RNA polymerase II (Cramer et al., 2001) established the mechanistic picture now organised under this topic, with elongation control emerging as a major regulatory layer.

Key figures

• Robert G. Roeder
• Roger Kornberg
• Patrick Cramer
• John T. Lis

Seminal works

• roeder-rutter-1969
• cramer-2001
• soutourina-2018

Frequently asked questions

Why do eukaryotes have three RNA polymerases?

The work of transcription is divided: RNA polymerase I makes most ribosomal RNA, RNA polymerase II makes messenger RNAs and many noncoding RNAs, and RNA polymerase III makes transfer RNAs and other small RNAs, each with its own machinery.

What is the preinitiation complex?

It is the assembly of RNA polymerase II together with the general transcription factors at a promoter that positions the enzyme, opens the DNA and prepares it to begin transcription.