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Unravelling the means to an end: RNA polymerase II transcription termination

Key Points

  • RNA polymerase II (Pol II) transcribes all eukaryotic protein-coding genes and most non-coding RNA genes. The final step of transcription is termination, which leads to the release of Pol II and RNA from the DNA template through a poorly defined mechanism.

  • Transcription termination serves many vital functions in the cell, such as preventing RNA polymerase interference with neighbouring DNA elements, recycling RNA polymerase, promoting RNA 3′-end processing, and regulating gene expression via premature termination of transcription (that is, attenuation).

  • Termination can be elicited through different pathways depending on the phosphorylation status of the Pol II carboxy-terminal domain (CTD) and the presence of various RNA signals and termination factors. Two of the best-studied termination pathways are the poly(A)-dependent pathway and Sen1-dependent pathway, which are connected to RNA 3′-end processing events for mRNAs and non-coding RNAs, respectively.

  • Three mechanisms are proposed to cause Pol II termination: conformational changes induced by binding of factors to Pol II; collision of an exoribonuclease with Pol II; and/or disruption of the Pol II active site hybrid by an RNA–DNA helicase. However, these molecular models have thus far remained insufficient to fully explain how termination occurs.

  • Pol II is similar both structurally and biochemically to bacterial RNA polymerase, suggesting that there may be some general features of termination that are common to all cellular RNA polymerases. Recent studies investigating the requirements for bacterial termination implicate several regions of Pol II as putative termination effector domains, including the lid, trigger loop, clamp helices, dock and flap.

  • The phosphorylation status of the Pol II CTD residues Ser7, Ser5 and Ser2 is dynamic across the length of a gene. Genome-wide localization studies suggest that a combination of high Ser7-P and Ser5-P and low Ser2-P in the CTD of Pol II at promoter-proximal positions may serve as a signal to trigger Sen1-dependent termination.

  • Genome-wide localization of protein 1 of CFI (Pcf11), Nrd1, and RNA-trafficking protein 1 (Rat1) reveals extensive overlap of these termination factors along both protein-coding and non-coding RNA genes. This pattern is consistent with the idea that the machinery for Sen1-dependent termination and poly(A)-dependent termination is broadly available to target Pol II during transcription of most genes, and in fact may provide a way to ensure fail-safe termination.


The pervasiveness of RNA synthesis in eukaryotes is largely the result of RNA polymerase II (Pol II)-mediated transcription, and termination of its activity is necessary to partition the genome and maintain the proper expression of neighbouring genes. Despite its ever-increasing biological significance, transcription termination remains one of the least understood processes in gene expression. However, recent mechanistic studies have revealed a striking convergence among several overlapping models of termination, including the poly(A)- and Sen1-dependent pathways, as well as new insights into the specificity of Pol II termination among its diverse gene targets. Broader knowledge of the role of Pol II carboxy-terminal domain phosphorylation in promoting alternative mechanisms of termination has also been gained.

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Figure 1: Pol II transcription is coordinated with distinct patterns of C-terminal domain phosphorylation.
Figure 2: Factors involved in poly(A)-dependent and Sen1-dependent termination.
Figure 3: Comparison of E. coli RNA polymerase and S. cerevisiae Pol II structures.
Figure 4: Genome-wide localization of yeast Pol II CTD phosphorylations and termination factors.


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Research in the laboratory of C.M. is supported by grants from the US National Institutes of Health National Institute of General Medical Sciences: award numbers K12GM074869 (J.N.K.), R01GM041752 (C.M.) and R01GM068887 (C.M.). We thank G. Meinke for assistance in preparing PyMOL images.

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Cryptic unstable transcripts

Non-coding RNAs (200–600 nucleotides long) discovered in yeast that are typically transcribed from intergenic regions of the genome (such as promoters) and are rapidly degraded by the exosome.

Stable unannotated transcripts

Non-coding RNAs discovered in yeast that are generally longer and more stable than cryptic unstable transcripts.

Promoter-proximal pausing

Halting of an early RNA polymerase elongation complex that remains competent to eventually resume transcription.

Genomic partitioning

Separation of adjacent DNA functional units from one another by transcription termination and/or DNA-binding proteins (such as chromatin) in order to prevent transcriptional interference.

Cleavage and polyadenylation specificity factor

A mammalian protein complex containing an endo-ribonuclease that is required for efficient mRNA 3′-end processing and RNA polymerase II (Pol II) transcription termination. Homologous to yeast cleavage and polyadenylation factor, which contains additional subunits required for efficient Pol II termination at small nuclear RNA-encoding and small nucleolar RNA-encoding genes.

Cleavage stimulatory factor

A mammalian protein complex that is required for efficient mRNA 3′-end processing and transcription termination. Homologous to yeast cleavage factor IA, which is also required for efficient RNA polymerase II termination at genes encoding small nuclear RNAs and small nucleolar RNAs.


A protein complex that targets various types of RNA for degradation primarily via its 3′–5′ exoribonuclease activity.


A polyadenylation complex that enhances exosome- mediated degradation of aberrant RNAs.


A ribonuclease III enzyme that initiates processing of microRNAs.

Tower domain

A pronounced and conserved α-helix near the active site of the yeast nuclear 5′–3′ exoribonuclease RNA-trafficking protein 1 (Rat1; XRN2 in mammals) but not its cytoplasmic orthologue 5′–3′ exoribonuclease 1 (Xrn1).


A technique that combines chromatin immunoprecipitation (ChIP) with microarray technology (chip) to investigate genome-wide protein–DNA interactions.

Prolyl isomerases

Enzymes that catalyse the interconversion of cis and trans isomers of peptide bonds with the amino acid Pro.

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Kuehner, J., Pearson, E. & Moore, C. Unravelling the means to an end: RNA polymerase II transcription termination. Nat Rev Mol Cell Biol 12, 283–294 (2011).

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