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Causes and consequences of RNA polymerase II stalling during transcript elongation

Nature Reviews Molecular Cell Biology volume 22, pages 3–21 (2021)Cite this article

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Abstract

The journey of RNA polymerase II (Pol II) as it transcribes a gene is anything but a smooth ride. Transcript elongation is discontinuous and can be perturbed by intrinsic regulatory barriers, such as promoter-proximal pausing, nucleosomes, RNA secondary structures and the underlying DNA sequence. More substantial blocking of Pol II translocation can be caused by other physiological circumstances and extrinsic obstacles, including other transcribing polymerases, the replication machinery and several types of DNA damage, such as bulky lesions and DNA double-strand breaks. Although numerous different obstacles cause Pol II stalling or arrest, the cell somehow distinguishes between them and invokes different mechanisms to resolve each roadblock. Resolution of Pol II blocking can be as straightforward as temporary backtracking and transcription elongation factor S-II (TFIIS)-dependent RNA cleavage, or as drastic as premature transcription termination or degradation of polyubiquitylated Pol II and its associated nascent RNA. In this Review, we discuss the current knowledge of how these different Pol II stalling contexts are distinguished by the cell, how they overlap with each other, how they are resolved and how, when unresolved, they can cause genome instability.

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Fig. 1: Nucleotide addition cycle and backtracking.
Fig. 2: Structural changes of Pol II during elongation, backtracking and pausing.
Fig. 3: Intrinsic barriers to transcript elongation.
Fig. 4: Conflicts involving RNA polymerase II during transcript elongation.
Fig. 5: Pol II degradation in response to ultraviolet light.
Fig. 6: Fates of stalled or arrested Pol II.

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Acknowledgements

The authors thank members of the Svejstrup laboratory for helpful comments and suggestions, and especially L. Gregersen and A. Tufegdzic Vidakovic for their critical reading of the manuscript. The authors apologize to those authors whose work could not be cited due to space constraints. M.N.G was supported by an EMBO Postdoctoral Fellowship (EMBO ALTF 2020-260).

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Author notes

  1. These authors contributed equally: Melvin Noe Gonzalez, Daniel Blears.

Authors and Affiliations

  1. Mechanisms of Transcription Laboratory, The Francis Crick Institute, London, UK

    Melvin Noe Gonzalez, Daniel Blears & Jesper Q. Svejstrup

  2. Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark

    Melvin Noe Gonzalez, Daniel Blears & Jesper Q. Svejstrup

Authors
  1. Melvin Noe Gonzalez
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  2. Daniel Blears
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  3. Jesper Q. Svejstrup
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The authors contributed equally to all aspects of the article.

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Correspondence to Jesper Q. Svejstrup.

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Glossary

General transcription factors

Transcription factors that are recruited to the promoter during transcription initiation and are necessary for the formation of the pre-initiation complex.

Pre-initiation complexes

(PICs). Complexes of general transcription factors and RNA polymerase II that assemble at gene promoters during transcription initiation.

Transcription pausing

Transient series of Pol II stalling events, followed by resumption of transcription.

Processive

Refers to the extent to which RNA polymerase II performs consecutive nucleotide incorporations and forward translocation without dissociating from the DNA.

Promoter-proximal pausing

Widespread, regulatory stalling of RNA polymerase II in animal cells shortly downstream of transcription start sites.

Transcription arrest

Blocking of transcript elongation by RNA polymerase II by an unsurmountable obstacle.

Genome instability

A cellular genotoxic state that may include changes in DNA sequence and/or chromosomal rearrangements.

Transcription stalling

The point at which forward translocation by RNA polymerase II is blocked, leading to secondary events that include backtracking, arrest or transcription resumption.

Transcription stress

Collective term for events in which RNA polymerase II becomes stalled or arrested during transcript elongation.

Premature termination

Termination of transcription anywhere between the transcription start site and the canonical polyadenylation site, by means of RNA cleavage and RNA polymerase II dissociation.

R-loop

Three-stranded RNA–DNA hybrid structure formed by hybridization of nascent RNA to the DNA strand from which it was transcribed.

Transcription start site

The DNA base position that is complimentary to the first incorporated RNA nucleoside triphosphate.

Pol II C-terminal domain

The highly conserved C-terminal domain (CTD) of RBP1, the catalytic subunit of RNA polymerase II (Pol II). Post-translational modification of the CTD is an important mechanism of transcription regulation.

Core promoter elements

Consensus DNA sequences located at gene promoters which direct the assembly of the pre-initiation complex and transcription initiation.

Nucleosome dyad

Central position within the nucleosome structure, at which a twofold topological symmetry is exhibited.

SHL

Superhelical locations on the nucleosome structure, spaced by approximately 10 bp. SHL(0) marks the nucleosome dyad.

Transcription readthrough

Continuation of transcription beyond (downstream) of canonical termination regions.

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Noe Gonzalez, M., Blears, D. & Svejstrup, J.Q. Causes and consequences of RNA polymerase II stalling during transcript elongation. Nat Rev Mol Cell Biol 22, 3–21 (2021). https://doi.org/10.1038/s41580-020-00308-8

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