Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II

Nature volume 432, pages 517–522 (2004)Cite this article

A Corrigendum to this article was published on 10 February 2005

Abstract

The carboxy-terminal domain (CTD) of the RNA polymerase II (RNApII) largest subunit consists of multiple heptapeptide repeats with the consensus sequence YSPTSPS. Different CTD phosphorylation patterns act as recognition sites for the binding of various messenger RNA processing factors, thereby coupling transcription and mRNA processing1. Polyadenylation factors are co-transcriptionally recruited by phosphorylation of CTD serine 2 (ref. 2) and these factors are also required for transcription termination3,4. RNApII transcribes past the poly(A) site, the RNA is cleaved by the polyadenylation machinery, and the RNA downstream of the cleavage site is degraded. Here we show that Rtt103 and the Rat1/Rai1 5′ → 3′ exonuclease are localized at 3′ ends of protein coding genes. In rat1-1 or rai1Δ cells, RNA 3′ to polyadenylation sites is greatly stabilized and termination defects are seen at many genes. These findings support a model in which poly(A) site cleavage and subsequent degradation of the 3′-downstream RNA by Rat1 trigger transcription termination5,6.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Isolation of a complex containing Rtt103, RNA polymerase II and the Rat1/Rai1 exonuclease.
Figure 2: Rtt103 and Rat1/Rai1 localize at 3′ ends of genes.
Figure 3: Rat1 degrades 3′-downstream RNA but is not required for mRNA cleavage or polyadenylation.
Figure 4: Rat1/Rai1 promotes transcription termination.

Similar content being viewed by others

References

  1. Buratowski, S. The CTD code. Nature Struct. Biol. 10, 679–680 (2003)

    Article  CAS  Google Scholar 

  2. Ahn, S. H., Kim, M. & Buratowski, S. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3′ end processing. Mol. Cell 13, 67–76 (2004)

    Article  CAS  Google Scholar 

  3. Birse, C. E., Minvielle-Sebastia, L., Lee, B. A., Keller, W. & Proudfoot, N. J. Coupling termination of transcription to messenger RNA maturation in yeast. Science 280, 298–301 (1998)

    Article  ADS  CAS  Google Scholar 

  4. Kim, M., Ahn, S. H., Krogan, N. J., Greenblatt, J. F. & Buratowski, S. Transitions in RNA polymerase II elongation complexes at the 3′ ends of genes. EMBO J. 23, 354–364 (2004)

    Article  CAS  Google Scholar 

  5. Connelly, S. & Manley, J. L. A CCAAT box sequence in the adenovirus major late promoter functions as part of an RNA polymerase II termination signal. Cell 57, 561–571 (1989)

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  7. Scholes, D. T., Banerjee, M., Bowen, B. & Curcio, M. J. Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance. Genetics 159, 1449–1465 (2001)

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Doerks, T., Copley, R. R., Schultz, J., Ponting, C. P. & Bork, P. Systematic identification of novel protein domain families associated with nuclear functions. Genome Res. 12, 47–56 (2002)

    Article  CAS  Google Scholar 

  9. Meinhart, A. & Cramer, P. Recognition of RNA polymerase II carboxy-terminal domain by 3′-RNA-processing factors. Nature 430, 223–226 (2004)

    Article  ADS  CAS  Google Scholar 

  10. Tong, A. H. et al. Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294, 2364–2368 (2001)

    Article  ADS  CAS  Google Scholar 

  11. Sterner, D. E., Lee, J. M., Hardin, S. E. & Greenleaf, A. L. The yeast carboxyl-terminal repeat domain kinase CTDK-I is a divergent cyclin-cyclin-dependent kinase complex. Mol. Cell. Biol. 15, 5716–5724 (1995)

    Article  CAS  Google Scholar 

  12. Skaar, D. A. & Greenleaf, A. L. The RNA polymerase II CTD kinase CTDK-I affects pre-mRNA 3′ cleavage/polyadenylation through the processing component Pti1p. Mol. Cell 10, 1429–1439 (2002)

    Article  CAS  Google Scholar 

  13. Dheur, S. et al. Pti1p and Ref2p found in association with the mRNA 3′ end formation complex direct snoRNA maturation. EMBO J. 22, 2831–2840 (2003)

    Article  CAS  Google Scholar 

  14. Nedea, E. et al. Organization and function of APT, a subcomplex of the yeast cleavage and polyadenylation factor involved in the formation of mRNA and small nucleolar RNA 3′-ends. J. Biol. Chem. 278, 33000–33010 (2003)

    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. Qu, L. H. et al. Seven novel methylation guide small nucleolar RNAs are processed from a common polycistronic transcript by Rat1p and RNase III in yeast. Mol. Cell. Biol. 19, 1144–1158 (1999)

    Article  CAS  Google Scholar 

  17. Xue, Y. et al. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. Mol. Cell. Biol. 20, 4006–4015 (2000)

    Article  CAS  Google Scholar 

  18. 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 

  19. Hammell, C. M. et al. Coupling of termination, 3′ processing, and mRNA export. Mol. Cell. Biol. 22, 6441–6457 (2002)

    Article  CAS  Google Scholar 

  20. Vasudevan, S. & Peltz, S. W. Nuclear mRNA surveillance. Curr. Opin. Cell Biol. 15, 332–337 (2003)

    Article  CAS  Google Scholar 

  21. Bousquet-Antonelli, C., Presutti, C. & Tollervey, D. Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102, 765–775 (2000)

    Article  CAS  Google Scholar 

  22. Das, B., Butler, J. S. & Sherman, F. Degradation of normal mRNA in the nucleus of Saccharomyces cerevisiae. Mol. Cell. Biol. 23, 5502–5515 (2003)

    Article  CAS  Google Scholar 

  23. Yonaha, M. & Proudfoot, N. J. Transcriptional termination and coupled polyadenylation in vitro. EMBO J. 19, 3770–3777 (2000)

    Article  CAS  Google Scholar 

  24. Holstege, F. C. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717–728 (1998)

    Article  CAS  Google Scholar 

  25. Solinger, J. A., Pascolini, D. & Heyer, W. D. Active-site mutations in the Xrn1p exoribonuclease of Saccharomyces cerevisiae reveal a specific role in meiosis. Mol. Cell. Biol. 19, 5930–5942 (1999)

    Article  CAS  Google Scholar 

  26. Ujvari, A., Pal, M. & Luse, D. S. RNA polymerase II transcription complexes may become arrested if the nascent RNA is shortened to less than 50 nucleotides. J. Biol. Chem. 277, 32527–32537 (2002)

    Article  CAS  Google Scholar 

  27. West, S., Gromak, N. & Proudfoot, N. Human 5′ → 3′ exonuclease XRN2 promotes transcription termination from co-transcriptional cleavage sites. Nature doi:10.1038/nature03035 (this issue)

  28. Krogan, N. J. et al. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol. Cell. Biol. 22, 6979–6992 (2002)

    Article  CAS  Google Scholar 

  29. Zhao, J., Kessler, M., Helmling, S., O'Connor, J. P. & Moore, C. Pta1, a component of yeast CF II, is required for both cleavage and poly(A) addition of mRNA precursor. Mol. Cell. Biol. 19, 7733–7740 (1999)

    Article  CAS  Google Scholar 

  30. Lashkari, D. A. et al. Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl Acad. Sci. USA 94, 13057–13062 (1997)

    Article  ADS  CAS  Google Scholar 

Download references

Acknowledgements

We thank C. Moore and her laboratory for advice on polyadenylation reactions; N. Proudfoot, S. McCracken and B. Blencowe for sharing unpublished information; and the Taplin Mass Spectroscopy facility at Harvard Medical School and D. Richards of Affinium Pharmaceuticals for mass spectroscopy. N.J.K. was supported by a Doctoral Fellowship from the Canadian Institutes of Health Research (CIHR). O.J.R. is supported by funding from the Bauer Center for Genomics Research. This research was supported by grants to S.B. from the US National Institutes of Health, and to J.F.G. from the Canadian Institutes of Health Research, the Ontario Genomics Institute, and the National Cancer Institute of Canada with funds from the Canadian Cancer Society. L.V. is a Fellow and S.B. is a Scholar of the Leukemia and Lymphoma Society.Authors’ contributions All authors contributed to the conception and design of the experiments. M.K. performed the CTD affinity purification of Rtt103, RT–PCR analysis, ChIP analyses and Rat1 mutagenesis. N.K. did the Rtt103-TAP purification and the SGA analysis. L.V. conducted the immunoblotting, exonuclease and polyadenylation assays. E.N. performed the Pcf11 and Rna15 TAP purifications. The microarray experiments were done by M.K. and O.J.R. The paper was written by M.K., J.G. and S.B. with input from the other authors.

Author information

Authors and Affiliations

  1. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts, 02115, USA

    Minkyu Kim, Lidia Vasiljeva & Stephen Buratowski

  2. Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario, M5G 1L6, Canada

    Nevan J. Krogan, Eduard Nedea & Jack F. Greenblatt

  3. Bauer Center for Genomics Research, Harvard University, 7 Divinity Ave., Cambridge, Massachusetts, 02138, USA

    Oliver J. Rando

Authors
  1. Minkyu Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Nevan J. Krogan
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lidia Vasiljeva
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Oliver J. Rando
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Eduard Nedea
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jack F. Greenblatt
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Stephen Buratowski
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Stephen Buratowski.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Figures 1 and 2

Fig 1: The termination defect in the rat1-1 mutant is not due to protein instability or defects in polyadenylation; Fig 2: The Rat1 D235A mutant lacks exonuclease activity. (DOC 81 kb)

Supplementary Table 1

The Rat1 D235A mutant lacks exonuclease activity. (DOC 26 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kim, M., Krogan, N., Vasiljeva, L. et al. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature 432, 517–522 (2004). https://doi.org/10.1038/nature03041

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature03041

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing