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Human 5′ → 3′ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites

Nature volume 432, pages 522–525 (2004)Cite this article

Abstract

Eukaryotic protein-encoding genes possess poly(A) signals that define the end of the messenger RNA and mediate downstream transcriptional termination by RNA polymerase II (Pol II)1. Termination could occur through an ‘anti-termination’ mechanism whereby elongation factors dissociate when the poly(A) signal is encountered, producing termination-competent Pol II2,3. An alternative ‘torpedo’ model postulated that poly(A) site cleavage provides an unprotected RNA 5′ end that is degraded by 5′ → 3′ exonuclease activities (torpedoes) and so induces dissociation of Pol II from the DNA template1,4. This model has been questioned because unprocessed transcripts read all the way to the site of transcriptional termination before upstream polyadenylation5,6,7. However, nascent transcripts located 1 kilobase downstream of the human β-globin gene poly(A) signal are associated with a co-transcriptional cleavage (CoTC) activity8 that acts with the poly(A) signal to elicit efficient transcriptional termination. The CoTC sequence is an autocatalytic RNA structure that undergoes rapid self-cleavage9. Here we show that CoTC acts as a precursor to termination by presenting a free RNA 5′ end that is recognized by the human 5′ → 3′ exonuclease Xrn2. Degradation of the downstream cleavage product by Xrn2 results in transcriptional termination, as envisaged in the torpedo model.

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Figure 1: RNAi-mediated depletion of human Xrn2 inhibits Pol II termination.
Figure 2: RNAi-mediated depletion of human Xrn2 protein increases steady-state read-through transcription.
Figure 3: Hammerhead ribozyme cleavage does not promote Xrn2-dependent termination.
Figure 4: Model for Pol II transcriptional termination.

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References

  1. Proudfoot, N. J. How RNA polymerase II terminates transcription in higher eukaryotes. Trends Biochem. Sci. 14, 105–110 (1989)

    Article  CAS  Google Scholar 

  2. Logan, J., Falck-Pedersen, E., Darnell, J. E. Jr & Shenk, T. A poly(A) addition site and a downstream termination region are required for efficient cessation of transcription by RNA polymerase II in the mouse beta maj-globin gene. Proc. Natl Acad. Sci. USA 84, 8306–8310 (1987)

    Article  ADS  CAS  Google Scholar 

  3. Proudfoot, N. New perspectives on connecting messenger RNA 3′ end formation to transcription. Curr. Opin. Cell Biol. 16, 272–278 (2004)

    Article  CAS  Google Scholar 

  4. Connelly, S. & Manley, J. L. A functional mRNA polyadenylation signal is required for transcription termination by RNA polymerase II. Genes Dev. 2, 440–452 (1988)

    Article  CAS  Google Scholar 

  5. Osheim, Y. N., Proudfoot, N. J. & Beyer, A. L. EM visualization of transcription by RNA polymerase II: downstream termination requires a poly(A) signal but not transcript cleavage. Mol. Cell 3, 379–387 (1999)

    Article  CAS  Google Scholar 

  6. Bauren, G., Belikov, S. & Wieslander, L. Transcriptional termination in the Balbiani ring 1 gene is closely coupled to 3′-end formation and excision of the 3′-terminal intron. Genes Dev. 12, 2759–2769 (1998)

    Article  CAS  Google Scholar 

  7. Dye, M. J. & Proudfoot, N. J. Terminal exon definition occurs cotranscriptionally and promotes termination of RNA polymerase II. Mol. Cell 3, 371–378 (1999)

    Article  CAS  Google Scholar 

  8. Dye, M. J. & Proudfoot, N. J. Multiple transcript cleavage precedes polymerase release in termination by RNA polymerase II. Cell 105, 669–681 (2001)

    Article  CAS  Google Scholar 

  9. Teixeira, A. et al. Auto-catalytic RNA cleavage in the human β-globin pre-mRNA promotes transcription termination. Nature doi:10.1038/nature03032 (this issue)

  10. Cerutti, H. RNA interference: travelling in the cell and gaining functions. Trends Genet. 19, 39–46 (2003)

    Article  CAS  Google Scholar 

  11. Zhang, M. et al. Cloning and mapping of the XRN2 gene to human chromosome 20p11.1–p11.2. Genomics 59, 252–254 (1999)

    Article  CAS  Google Scholar 

  12. Lejeune, F., Li, X. & Maquat, L. E. Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities. Mol. Cell 12, 675–687 (2003)

    Article  CAS  Google Scholar 

  13. Amberg, D. C., Goldstein, A. L. & Cole, C. N. Isolation and characterization of RAT1: an essential gene of Saccharomyces cerevisiae required for the efficient nucleocytoplasmic trafficking of mRNA. Genes Dev. 6, 1173–1189 (1992)

    Article  CAS  Google Scholar 

  14. Henry, Y. et al. The 5′ end of yeast 5.8S rRNA is generated by exonucleases from an upstream cleavage site. EMBO J. 13, 2452–2463 (1994)

    Article  CAS  Google Scholar 

  15. Petfalski, E., Dandekar, T., Henry, Y. & Tollervey, D. Processing of the precursors to small nucleolar RNAs and rRNAs requires common components. Mol. Cell. Biol. 18, 1181–1189 (1998)

    Article  CAS  Google Scholar 

  16. Strausberg, R. L. et al. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc. Natl Acad. Sci. USA 99, 16899–16903 (2002)

    Article  ADS  Google Scholar 

  17. Samarsky, D. A. et al. A small nucleolar RNA:ribozyme hybrid cleaves a nucleolar RNA target in vivo with near-perfect efficiency. Proc. Natl Acad. Sci. USA 96, 6609–6614 (1999)

    Article  ADS  CAS  Google Scholar 

  18. Huertas, P. & Aguilera, A. Cotranscriptionally formed DNA:RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol. Cell 12, 711–721 (2003)

    Article  CAS  Google Scholar 

  19. Hammann, C. & Lilley, D. M. Folding and activity of the hammerhead ribozyme. Chembiochem 3, 690–700 (2002)

    Article  CAS  Google Scholar 

  20. Stevens, A. & Poole, T. L. 5′ exonuclease 2 of Saccharomyces cerevisiae. J. Biol. Chem. 270, 16063–16069 (1995)

    Article  CAS  Google Scholar 

  21. Torchet, C. et al. Processing of 3′-extended read-through transcripts by the exosome can generate functional mRNAs. Mol. Cell 9, 1285–1296 (2002)

    Article  CAS  Google Scholar 

  22. Kim, M. et al. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature doi:10.1038/nature03041 (this issue)

  23. Adams, S. E. et al. Synthesis of a gene for the HIV transactivator protein TAT by a novel single-stranded approach involving in vivo gap repair. Nucleic Acids Res. 16, 4287–4298 (1988)

    Article  ADS  CAS  Google Scholar 

  24. Ashe, H. L., Monks, J., Wijgerde, M., Fraser, P. & Proudfoot, N. J. Intergenic transcription and transinduction of the human β-globin locus. Genes Dev. 11, 2494–2509 (1997)

    Article  CAS  Google Scholar 

  25. Wagner, E. J. & Garcia-Blanco, M. A. RNAi-mediated PTB depletion leads to enhanced exon definition. Mol. Cell 10, 943–949 (2002)

    Article  CAS  Google Scholar 

  26. Wollerton, M. C., Gooding, C., Wagner, E. J., Garcia-Blanco, M. A. & Smith, C. W. Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay. Mol. Cell 13, 91–100 (2004)

    Article  CAS  Google Scholar 

  27. Kadener, S., Fededa, J. P., Rosbash, M. & Kornblihtt, A. R. Regulation of alternative splicing by a transcriptional enhancer through RNA pol II elongation. Proc. Natl Acad. Sci. USA 99, 8185–8190 (2002)

    Article  ADS  CAS  Google Scholar 

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Acknowledgements

We thank M. Dye for expert advice on NRO analysis, M. Wollerton for advice on RNAi, I. Martianov for help with the western blot, L. Maquat and F. Lejeune for providing Xrn2 antibody, and A. Teixeira, A. Akoulitchev and members of N.J.P's laboratory for advice and encouragement. This work was supported by a Programme Grant from the Wellcome Trust.

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  1. Steven West and Natalia Gromak: These authors contributed equally to this work

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  1. Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, Oxford, UK

    Steven West, Natalia Gromak & Nick J. Proudfoot

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Correspondence to Nick J. Proudfoot.

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West, S., Gromak, N. & Proudfoot, N. Human 5′ → 3′ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites. Nature 432, 522–525 (2004). https://doi.org/10.1038/nature03035

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