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Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

Abstract

Pervasive and hidden transcription is widespread in eukaryotes1,2,3,4, but its global level, the mechanisms from which it originates and its functional significance are unclear. Cryptic unstable transcripts (CUTs) were recently described as a principal class of RNA polymerase II transcripts in Saccharomyces cerevisiae5. These transcripts are targeted for degradation immediately after synthesis by the action of the Nrd1–exosome–TRAMP complexes6,7. Although CUT degradation mechanisms have been analysed in detail, the genome-wide distribution at the nucleotide resolution and the prevalence of CUTs are unknown. Here we report the first high-resolution genomic map of CUTs in yeast, revealing a class of potentially functional CUTs and the intrinsic bidirectional nature of eukaryotic promoters. An RNA fraction highly enriched in CUTs was analysed by a 3′ Long-SAGE (serial analysis of gene expression) approach adapted to deep sequencing. The resulting detailed genomic map of CUTs revealed that they derive from extremely widespread and very well defined transcription units and do not result from unspecific transcriptional noise. Moreover, the transcription of CUTs predominantly arises within nucleosome-free regions, most of which correspond to promoter regions of bona fide genes. Some of the CUTs start upstream from messenger RNAs and overlap their 5′ end. Our study of glycolysis genes, as well as recent results from the literature8,9,10,11, indicate that such concurrent transcription is potentially associated with regulatory mechanisms. Our data reveal numerous new CUTs with such a potential regulatory role. However, most of the identified CUTs corresponded to transcripts divergent from the promoter regions of genes, indicating that they represent by-products of divergent transcription occurring at many and possibly most promoters. Eukaryotic promoter regions are thus intrinsically bidirectional, a fundamental property that escaped previous analyses because in most cases divergent transcription generates short-lived unstable transcripts present at very low steady-state levels.

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Figure 1: Genome-wide analyses of 3′ SAGE-tag clusters.
Figure 2: Regulation of CUTs associated with TPI1 mRNAs.
Figure 3: Distribution of TA CUTs relative to NFRs.

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ArrayExpress

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Raw data are available from ArrayExpress (http://www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-75 for SAGE data and E-TABM-602 for tiling array data.

References

  1. Davis, C. A. & Ares, M. Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae . Proc. Natl Acad. Sci. USA 103, 3262–3267 (2006)

    ADS  CAS  Article  Google Scholar 

  2. Johnson, J. M., Edwards, S., Shoemaker, D. & Schadt, E. E. Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends Genet. 21, 93–102 (2005)

    CAS  Article  Google Scholar 

  3. Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science 296, 916–919 (2002)

    ADS  CAS  Article  Google Scholar 

  4. Kapranov, P. et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316, 1484–1488 (2007)

    ADS  CAS  Article  Google Scholar 

  5. Wyers, F. et al. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121, 725–737 (2005)

    CAS  Article  Google Scholar 

  6. Arigo, J. T., Eyler, D. E., Carroll, K. L. & Corden, J. L. Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3. Mol. Cell 23, 841–851 (2006)

    CAS  Article  Google Scholar 

  7. Thiebaut, M., Kisseleva-Romanova, E., Rougemaille, M., Boulay, J. & Libri, D. Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the Nrd1–Nab3 pathway in genome surveillance. Mol. Cell 23, 853–864 (2006)

    CAS  Article  Google Scholar 

  8. Kuehner, J. N. & Brow, D. A. Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation. Mol. Cell 31, 201–211 (2008)

    CAS  Article  Google Scholar 

  9. Martens, J. A., Laprade, L. & Winston, F. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429, 571–574 (2004)

    ADS  CAS  Article  Google Scholar 

  10. Martens, J. A., Wu, P. Y. & Winston, F. Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae . Genes Dev. 19, 2695–2704 (2005)

    CAS  Article  Google Scholar 

  11. Thiebaut, M. et al. Futile cycle of transcription initiation and termination modulates the response to nucleotide shortage in S. cerevisiae . Mol. Cell 31, 671–682 (2008)

    CAS  Article  Google Scholar 

  12. Rigaut, G. et al. A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnol. 17, 1030–1032 (1999)

    CAS  Article  Google Scholar 

  13. Wei, C. L. et al. 5′ Long serial analysis of gene expression (LongSAGE) and 3′ LongSAGE for transcriptome characterization and genome annotation. Proc. Natl Acad. Sci. USA 101, 11701–11706 (2004)

    ADS  CAS  Article  Google Scholar 

  14. 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)

    CAS  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  16. David, L. et al. A high-resolution map of transcription in the yeast genome. Proc. Natl Acad. Sci. USA 103, 5320–5325 (2006)

    ADS  CAS  Article  Google Scholar 

  17. Arigo, J. T., Carroll, K. L., Ames, J. M. & Corden, J. L. Regulation of yeast NRD1 expression by premature transcription termination. Mol. Cell 21, 641–651 (2006)

    CAS  Article  Google Scholar 

  18. Scott, E. W. & Baker, H. V. Concerted action of the transcriptional activators REB1, RAP1, and GCR1 in the high-level expression of the glycolytic gene TPI . Mol. Cell. Biol. 13, 543–550 (1993)

    CAS  Article  Google Scholar 

  19. Camblong, J., Iglesias, N., Fickentscher, C., Dieppois, G. & Stutz, F. Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae . Cell 131, 706–717 (2007)

    CAS  Article  Google Scholar 

  20. Teodorovic, S., Walls, C. D. & Elmendorf, H. G. Bidirectional transcription is an inherent feature of Giardia lamblia promoters and contributes to an abundance of sterile antisense transcripts throughout the genome. Nucleic Acids Res. 35, 2544–2553 (2007)

    CAS  Article  Google Scholar 

  21. Lee, W. et al. A high-resolution atlas of nucleosome occupancy in yeast. Nature Genet. 39, 1235–1244 (2007)

    CAS  Article  Google Scholar 

  22. Ito, T., Miura, F. & Onda, M. Unexpected complexity of the budding yeast transcriptome. IUBMB Life 60, 775–781 (2008)

    CAS  Article  Google Scholar 

  23. Struhl, K. Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nature Struct. Mol. Biol. 14, 103–105 (2007)

    CAS  Article  Google Scholar 

  24. Whitehouse, I., Rando, O. J., Delrow, J. & Tsukiyama, T. Chromatin remodelling at promoters suppresses antisense transcription. Nature 450, 1031–1035 (2007)

    ADS  CAS  Article  Google Scholar 

  25. Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008)

    ADS  CAS  Article  Google Scholar 

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Acknowledgements

We thank D. Libri for the gift of strains, D. Libri, C. Thermes, C. Saveanu and M. Fromont-Racine for discussions and for critical reading of the manuscript, staff of the Genoscope (Evry) for sequencing, and A. Doyen, L. Decourty, S. Clauder-Muenster and T. Bähr-Ivacevic for technical assistance. This work was supported by the Institut Pasteur, the CNRS, the ANR (CUT program), the European Science Foundation (RNA quality program), and the National Institutes of Health and the Deutsche Forschungsgemeinschaft. H.N. is supported by the ANR (CUT program).

Author Contributions H.N. performed the experimental work except the sequencing, which was performed at Genoscope, Evry, and the tiling array experiments, which were performed in the group of L.M.S. and analysed by Z.X.; C.M. performed most of the bioinformatics analyses with the help of Y.d’A.-C. for the NFRs analyses; A.J. and H.N. designed the research and A.J. supervised the work; and A.J., H.N. and C.M. wrote the manuscript.

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Correspondence to Alain Jacquier.

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This file contains Supplementary Figures S1-S10 with Legends, Supplementary Methods, Supplementary Data, Supplementary Tables 1-5 and Supplementary References (PDF 4680 kb)

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Neil, H., Malabat, C., d’Aubenton-Carafa, Y. et al. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457, 1038–1042 (2009). https://doi.org/10.1038/nature07747

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