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RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts

Nature volume 413, pages 327–331 (2001)Cite this article

Abstract

A eukaryotic chromosome contains many genes, each transcribed separately by RNA polymerase (pol) I, II or III. Transcription termination between genes prevents the formation of polycistronic RNAs and anti-sense RNAs, which are generally detrimental to the correct expression of genes. Terminating the transcription of protein-coding genes by pol II requires a group of proteins that also direct cleavage and polyadenylation of the messenger RNA in response to a specific sequence element, and are associated with the carboxyl-terminal domain of the largest subunit of pol II (refs 1, 2, 3, 4, 5, 6). By contrast, the cis-acting elements and trans-acting factors that direct termination of non-polyadenylated transcripts made by pol II, including small nucleolar and small nuclear RNAs, are not known. Here we show that read-through transcription from yeast small nucleolar RNA and small nuclear RNA genes into adjacent genes is prevented by a cis-acting element that is recognized, in part, by the essential RNA-binding protein Nrd1. The RNA-binding protein Nab3, the putative RNA helicase Sen1, and the intact C-terminal domain of pol II are also required for efficient response to the element. The same proteins are required for maintaining normal levels of Nrd1 mRNA, indicating that these proteins may control elongation of a subset of mRNA transcripts.

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Figure 1: ′3-extended snoRNA transcripts are produced in nrd1 and other mutant strains.
Figure 2: Termination of SNR3 transcription is impaired in a nrd1 strain.
Figure 3: Nrd1-dependent 3′-end formation elements from SNR13 and SNR14 (U4 snRNA) genes.
Figure 4: Autoregulation of Nrd1 mRNA accumulation by the Nrd1-dependent 3′-end formation pathway.

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References

  1. McCracken, S. et al. The C-terminal domain of RNA polymerase II couples mRNA processing to transcription. Nature 385, 357–361 (1997).

    Article  ADS  CAS  Google Scholar 

  2. 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 

  3. Hirose, Y. & Manley, J. L. RNA polymerase II is an essential mRNA polyadenylation factor. Nature 395, 93–96 (1998).

    Article  ADS  CAS  Google Scholar 

  4. 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 

  5. Rodriguez, C. R. et al. Kin28, the TFIIH-associated carboxy-terminal domain kinase, facilitates the recruitment of mRNA processing machinery to RNA polymerase II. Mol. Cell. Biol. 20, 104–112 (2000).

    Article  CAS  Google Scholar 

  6. Barilla, D., Lee, B. A. & Proudfoot, N. J. Cleavage/polyadenylation factor IA associates with the carboxyl-terminal domain of RNA polymerase II in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 98, 445–450 (2001).

    ADS  CAS  Google Scholar 

  7. Steinmetz, E. J. & Brow, D. A. Repression of gene expression by an exogenous sequence element acting in concert with a heterogeneous nuclear ribonucleoprotein-like protein, Nrd1, and the putative helicase Sen1. Mol. Cell. Biol. 16, 6993–7003 (1996).

    Article  CAS  Google Scholar 

  8. Steinmetz, E. J. & Brow, D. A. Control of pre-mRNA accumulation by the essential yeast protein Nrd1 requires high-affinity transcript binding and a domain implicated in RNA polymerase II association. Proc. Natl Acad. Sci. USA 95, 6699–6704 (1998).

    Article  ADS  CAS  Google Scholar 

  9. DeMarini, D. J., Winey, M., Ursic, D., Webb, F. & Culbertson, M. R. SEN1, a positive effector of tRNA-splicing endonuclease in Saccharomyces cerevisiae. Mol. Cell. Biol. 12, 2154–2164 (1992).

    Article  CAS  Google Scholar 

  10. Ursic, D., Himmel, K. L., Gurley, K. A., Webb, F. & Culbertson, M. R. The yeast SEN1 gene is required for the processing of diverse RNA classes. Nucleic Acids Res. 25, 4778–4785 (1997).

    Article  CAS  Google Scholar 

  11. Rasmussen, T. P. & Culbertson, M. R. The putative nucleic acid helicase Sen1p is required for formation and stability of termini and for maximal rates of synthesis and levels of accumulation of small nucleolar RNAs in Saccharomyces cerevisiae. Mol. Cell. Biol. 18, 6885–6896 (1998); erratum ibid. 19, 5235 (1999).

    Article  CAS  Google Scholar 

  12. Greger, I. H., Aranda, A. & Proudfoot, N. Balancing transcriptional interference and initiation on the GAL7 promoter of Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 97, 8415–8420 (2000).

    Article  ADS  CAS  Google Scholar 

  13. Yuryev, A. et al. The C-terminal domain of the largest subunit of RNA polymerase II interacts with a novel set of serine/arginine-rich proteins. Proc. Natl Acad. Sci. USA 93, 6975–6980 (1996).

    Article  ADS  CAS  Google Scholar 

  14. Conrad, N. K. et al. A yeast heterogeneous nuclear ribonucleoprotein complex associated with RNA polymerase II. Genetics 154, 557–571 (2000).

    CAS  Google Scholar 

  15. Lee, J. M. & Greenleaf, A. L. CTD kinase large subunit is encoded by CTK1, a gene required for normal growth of Saccharomyces cerevisiae. Gene Expr. 1, 149–167 (1991).

    CAS  Google Scholar 

  16. Allmang, C. et al. Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J. 18, 5399–5410 (1999).

    Article  CAS  Google Scholar 

  17. van Hoof, A., Lennertz, P. & Parker, R. Yeast exosome mutants accumulate 3′-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol. Cell. Biol. 20, 441–452 (2000).

    Article  CAS  Google Scholar 

  18. Fatica, A., Morlando, M. & Bozzoni, I. Yeast snoRNA accumulation relies on a cleavage-dependent/polyadenylation-independent 3′-processing apparatus. EMBO J. 19, 6218–6229 (2000).

    Article  CAS  Google Scholar 

  19. Lesser, C. F. & Guthrie, C. Mutational analysis of pre-mRNA splicing in Saccharomyces cerevisiae using a sensitive new reporter gene, CUP1. Genetics 133, 851–863 (1993).

    CAS  Google Scholar 

  20. Chanfreau, G., Elela, S. A., Ares, M. Jr & Guthrie, C. Alternative 3′-end processing of U5 snRNA by RNase III. Genes Dev. 11, 2741–2751 (1997).

    Article  CAS  Google Scholar 

  21. Abou Elela, S. & Ares, M. Jr Depletion of yeast RNase III blocks correct U2 3′ end formation and results in polyadenylated but functional U2 snRNA. EMBO J. 17, 3738–3746 (1998).

    Article  CAS  Google Scholar 

  22. Seipelt, R. L., Zheng, B., Asuru, A. & Rymond, B. C. U1 snRNA is cleaved by RNase III and processed through an Sm site-dependent pathway. Nucleic Acids Res. 27, 587–595 (1999).

    Article  CAS  Google Scholar 

  23. Sacher, M., Barrowman, J., Schieltz, D., Yates, J. R. III & Ferro-Novick, S. Identification and characterization of five new subunits of TRAPP. Eur. J. Cell. Biol. 79, 71–80 (2000).

    Article  CAS  Google Scholar 

  24. Trotta, C. R. et al. The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases. Cell 89, 849–858 (1997).

    Article  CAS  Google Scholar 

  25. West, M. L. & Corden, J. L. Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutations. Genetics 140, 1223–1233 (1995).

    CAS  Google Scholar 

  26. Brachmann, C. B. et al. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14, 115–132 (1998).

    Article  CAS  Google Scholar 

  27. Mumberg, D., Muller, R. & Funk, M. Regulatable promoters of Saccharomyces cerevisiae: comparison of transcriptional activity and their use for heterologous expression. Nucleic Acids Res. 22, 5767–5768 (1994).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank J. Dahlberg and J. Boeke for critically reviewing the manuscript, and members of the Brow, Corden and M. Culbertson labs for discussions. We also thank C. Colantuoni and J. Pevsner for assistance with the expression profiling experiments. This work was supported by grants from the NIH and the NSF.

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Author notes

  1. Eric J. Steinmetz, Nicholas K. Conrad and Jeffry L. Corden: These authors contributed equally to this work

Authors and Affiliations

  1. Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, 53706-1532, Wisconsin, USA

    Eric J. Steinmetz & David A. Brow

  2. Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, 21205, Maryland, USA

    Nicholas K. Conrad & Jeffry L. Corden

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  1. Eric J. Steinmetz
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  2. Nicholas K. Conrad
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Correspondence to David A. Brow.

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Steinmetz, E., Conrad, N., Brow, D. et al. RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts. Nature 413, 327–331 (2001). https://doi.org/10.1038/35095090

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