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Updated: Apr 14, 2026

Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on TRO Approach
Published on: March 12, 2017
Pcf11 orchestrates transcription termination pathways in yeast
Pawel Grzechnik1, Michal Ryszard Gdula2, Nick J Proudfoot3
1Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom;
The NRD complex, including Nrd1, Nab3, and Sen1, terminates transcription of short noncoding RNAs (ncRNAs) in yeast. Pcf11 is also crucial for this NRD-dependent termination, facilitating RNA polymerase II pausing and Sen1 activity.
Area of Science:
- Molecular Biology
- Yeast Genetics
- RNA Biology
Background:
- Short noncoding RNAs (ncRNAs) in Saccharomyces cerevisiae are terminated by the NRD complex (Nrd1, Nab3, Sen1).
- RNA polymerase II (Pol II) generates these ncRNAs.
Purpose of the Study:
- To investigate the role of Pcf11, a component of the cleavage and polyadenylation complex (CPAC), in NRD-dependent transcription termination.
- To elucidate the mechanism by which Pcf11 interacts with the NRD complex.
Main Methods:
- Genetic analysis of yeast mutants (pcf11, sen1).
- Chromatin localization studies of NRD complex components.
- Analysis of Pol II CTD phosphorylation and protein interactions.
- RNA:DNA hybrid detection.
Main Results:
- Pcf11 is generally required for NRD-dependent transcription termination via its CTD-interacting domain (CID).
- Pcf11 localizes downstream of Nrd1 on terminators, dependent on Nrd1 recruitment.
- Pcf11 CID mutations cause Nrd1 retention, delayed ncRNA degradation, and altered Pol II CTD Ser2 phosphorylation and Sen1 interaction.
- pcf11 and sen1 mutants exhibit similar phenotypes, including RNA:DNA hybrid accumulation and Pol II pausing.
Conclusions:
- Pcf11 acts with the NRD complex for transcription termination.
- A proposed mechanism involves Nrd1/Pcf11 exchange on chromatin, promoting Pol II pausing and CTD phosphorylation, which enhances Sen1 activity for termination.
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