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Structural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases

Nature Reviews Molecular Cell Biology volume 23, pages 603–622 (2022)Cite this article

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Abstract

The eukaryotic transcription apparatus synthesizes a staggering diversity of RNA molecules. The labour of nuclear gene transcription is, therefore, divided among multiple DNA-dependent RNA polymerases. RNA polymerase I (Pol I) transcribes ribosomal RNA, Pol II synthesizes messenger RNAs and various non-coding RNAs (including long non-coding RNAs, microRNAs and small nuclear RNAs) and Pol III produces transfer RNAs and other short RNA molecules. Pol I, Pol II and Pol III are large, multisubunit protein complexes that associate with a multitude of additional factors to synthesize transcripts that largely differ in size, structure and abundance. The three transcription machineries share common characteristics, but differ widely in various aspects, such as numbers of RNA polymerase subunits, regulatory elements and accessory factors, which allows them to specialize in transcribing their specific RNAs. Common to the three RNA polymerases is that the transcription process consists of three major steps: transcription initiation, transcript elongation and transcription termination. In this Review, we outline the common principles and differences between the Pol I, Pol II and Pol III transcription machineries and discuss key structural and functional insights obtained into the three stages of their transcription processes.

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Fig. 1: Transcription by eukaryotic RNA polymerases I, II and III.
Fig. 2: Structures of RNA polymerases I, II and III and of their general transcription factors.
Fig. 3: Organization of genes and promoters of RNA polymerases I, II and III.
Fig. 4: Transcription initiation.
Fig. 5: Transcript elongation and co-transcriptional RNA processing.
Fig. 6: Transcription termination.

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Acknowledgements

This work was supported by the European Molecular Biology Laboratory (M.G., A.D.M. and C.W.M.) and the European Molecular Biology Laboratory International PhD Programme (M.G. and A.D.M.). The authors thank F. Baudin for feedback on the manuscript. M.G. acknowledges support from a Boehringer Ingelheim Fonds PhD fellowship. The authors apologize to those authors whose work has not been included because of space limitations.

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  1. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

    Mathias Girbig, Agata D. Misiaszek & Christoph W. Müller

  2. Faculty of Biosciences, Heidelberg University, Heidelberg, Germany

    Agata D. Misiaszek

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  1. Mathias Girbig
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  2. Agata D. Misiaszek
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  3. Christoph W. Müller
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All authors contributed equally to this article.

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Correspondence to Christoph W. Müller.

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Glossary

Active site

A common term for the catalytic centre of RNA polymerases.

Stalk

A mobile structural element found in archaeal and eukaryotic RNA polymerases that is composed of one or two subunits and functions in transcription initiation.

Alu elements

Short, primate-specific transposons transcribed by RNA polymerase III (Pol III) or Pol II.

Microsatellites

Tandem repeats of 1–6 bp that are often used as genetic markers.

Transposons

Mobile DNA elements that can relocate within the genome.

Spacer promoters

Sequences in the spacer regions of ribosomal DNA repeats adjacent to ribosomal DNA promoters, with which they share a high degree of similarity.

Proximal terminators

Terminator elements directly upstream of ribosomal RNA gene promoters which prevent readthrough of polymerases from the intergenic spacer into the promoter that is bound by the stable RNA polymerase I (Pol I) preinitiation complex.

R-loops

Three-stranded RNA–DNA hybrid structures that form when a transcribed RNA invades the double-stranded DNA and hybridizes with its complementary template strand, thereby rendering the non-template single-stranded.

Terminator sequences

Nucleic acid sequences that mark the end of a gene and stimulate transcription termination.

Activator-dependent promoter

Promoter element that exerts high and specific promoter activity only when accompanied by additional motifs bound by other activators.

Stably positioned nucleosomes

Nucleosomes that are stably (strongly) positioned in the genome across many cells.

Dynamic nucleosomes

Nucleosomes whose positions are fuzzy owing to, for example, DNA sequences or activity of chromatin remodellers.

Dock

A small protein domain found in subunit A190 of RNA polymerase I (Pol I), subunit RPB1 of Pol II and subunit C160 of Pol III, which serves as a binding platform for transcription initiation factors.

Clamp domain

A mobile protein domain found in all DNA-dependent RNA polymerases that adopts an ‘open’ conformation in DNA-unbound polymerases, but closes upon DNA binding, and thereby participates in various steps during the transcription process.

Ribosome processomes

Large ribonucleoprotein complexes formed between the pre-ribosomal RNA, ribosomal proteins and RNA-processing factors during the process of ribosome maturation.

Funnel

Structural element of RNA polymerases that serves as the entry channel for nucleoside triphosphates and the exit channel for the RNA 3′ end, which is expelled from the active site upon polymerase backtracking.

Backtracking

RNA polymerase backward movement owing to stalling (for example, due to nucleotide misincorporation), which requires intrinsic or extrinsic RNA cleavage to restore transcript elongation.

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Girbig, M., Misiaszek, A.D. & Müller, C.W. Structural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases. Nat Rev Mol Cell Biol 23, 603–622 (2022). https://doi.org/10.1038/s41580-022-00476-9

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