XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast (original) (raw)

Nature volume 475, pages 114–117 (2011)Cite this article

Subjects

Abstract

Non-coding (nc)RNAs are key players in numerous biological processes such as gene regulation, chromatin domain formation and genome stability1,2. Large ncRNAs interact with histone modifiers3,4,5 and are involved in cancer development6, X-chromosome inactivation7 and autosomal gene imprinting8. However, despite recent evidence showing that pervasive transcription is more widespread than previously thought9, only a few examples mediating gene regulation in eukaryotes have been described10. In Saccharomyces cerevisiae, the bona-fide regulatory ncRNAs are destabilized by the Xrn1 5′–3′ RNA exonuclease11,12 (also known as Kem1), but the genome-wide characterization of the entire regulatory ncRNA family remains elusive. Here, using strand-specific RNA sequencing (RNA-seq), we identify a novel class of 1,658 Xrn1-sensitive unstable transcripts (XUTs) in which 66% are antisense to open reading frames. These transcripts are polyadenylated and RNA polymerase II (RNAPII)-dependent. The majority of XUTs strongly accumulate in lithium-containing media, indicating that they might have a role in adaptive responses to changes in growth conditions. Notably, RNAPII chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) analysis of Xrn1-deficient strains revealed a significant decrease of RNAPII occupancy over 273 genes with antisense XUTs. These genes show an unusual bias for H3K4me3 marks and require the Set1 histone H3 lysine 4 methyl-transferase for silencing. Furthermore, abolishing H3K4me3 triggers the silencing of other genes with antisense XUTs, supporting a model in which H3K4me3 antagonizes antisense ncRNA repressive activity. Our results demonstrate that antisense ncRNA-mediated regulation is a general regulatory pathway for gene expression in S. cerevisiae.

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

Access options

Subscribe to this journal

Receive 51 print issues and online access

$199.00 per year

only $3.90 per issue

Buy this article

USD 39.95

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

Additional access options:

Similar content being viewed by others

Accession codes

Primary accessions

Sequence Read Archive

Data deposits

Sequence data are publicly available at NCBI Sequence Read Archive under accession number SRA030505 and at http://vm-gb.curie.fr/XUT/index.htm.

References

  1. Bernstein, E. & Allis, C. D. RNA meets chromatin. Genes Dev. 19, 1635–1655 (2005)
    Article CAS Google Scholar
  2. Moazed, D. Small RNAs in transcriptional gene silencing and genome defence. Nature 457, 413–420 (2009)
    Article ADS CAS Google Scholar
  3. Swiezewski, S., Liu, F., Magusin, A. & Dean, C. Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462, 799–802 (2009)
    Article ADS CAS Google Scholar
  4. Yu, W. et al. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451, 202–206 (2008)
    Article ADS CAS Google Scholar
  5. Yap, K. L. et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a . Mol. Cell 38, 662–674 (2010)
    Article CAS Google Scholar
  6. Huarte, M. & Rinn, J. L. Large non-coding RNAs: missing links in cancer? Hum. Mol. Genet. 19, R152–R161 (2010)
    Article CAS Google Scholar
  7. Chow, J. & Heard, E. X inactivation and the complexities of silencing a sex chromosome. Curr. Opin. Cell Biol. 21, 359–366 (2009)
    Article CAS Google Scholar
  8. Nagano, T. et al. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322, 1717–1720 (2008)
    Article ADS CAS Google Scholar
  9. Amaral, P. P., Dinger, M. E., Mercer, T. R. & Mattick, J. S. The eukaryotic genome as an RNA machine. Science 319, 1787–1789 (2008)
    Article ADS CAS Google Scholar
  10. Berretta, J. & Morillon, A. Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep. 10, 973–982 (2009)
    Article CAS Google Scholar
  11. Camblong, J. et al. _Trans_-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae . Genes Dev. 23, 1534–1545 (2009)
    Article CAS Google Scholar
  12. Berretta, J., Pinskaya, M. & Morillon, A. A cryptic unstable transcript mediates transcriptional _trans_-silencing of the Ty1 retrotransposon in S. cerevisiae . Genes Dev. 22, 615–626 (2008)
    Article CAS Google Scholar
  13. Matsuda, E. & Garfinkel, D. J. Posttranslational interference of Ty1 retrotransposition by antisense RNAs. Proc. Natl Acad. Sci. USA 106, 15657–15662 (2009)
    Article ADS CAS Google Scholar
  14. Aravind, L., Watanabe, H., Lipman, D. J. & Koonin, E. V. Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc. Natl Acad. Sci. USA 97, 11319–11324 (2000)
    Article ADS CAS Google Scholar
  15. Jacquier, A. The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nature Rev. Genet. 10, 833–844 (2009)
    Article CAS Google Scholar
  16. Long, R. M. & McNally, M. T. mRNA decay: X (XRN1) marks the spot. Mol. Cell 11, 1126–1128 (2003)
    Article CAS Google Scholar
  17. Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008)
    Article ADS CAS Google Scholar
  18. Neil, H. et al. Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457, 1038–1042 (2009)
    Article ADS CAS Google Scholar
  19. Yassour, M. et al. Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol. 11, R87 (2010)
    Article Google Scholar
  20. Chernyakov, I., Whipple, J. M., Kotelawala, L., Grayhack, E. J. & Phizicky, E. M. Degradation of several hypomodified mature tRNA species in Saccharomyces cerevisiae is mediated by Met22 and the 5′–3′ exonucleases Rat1 and Xrn1. Genes Dev. 22, 1369–1380 (2008)
    Article CAS Google Scholar
  21. 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
  22. Xu, Z. et al. Bidirectional promoters generate pervasive transcription in yeast. Nature 457, 1033–1037 (2009)
    Article ADS CAS Google Scholar
  23. Thompson, D. M. & Parker, R. Cytoplasmic decay of intergenic transcripts in Saccharomyces cerevisiae . Mol. Cell. Biol. 27, 92–101 (2007)
    Article CAS Google Scholar
  24. 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)
    Article CAS Google Scholar
  25. Dichtl, B., Stevens, A. & Tollervey, D. Lithium toxicity in yeast is due to the inhibition of RNA processing enzymes. EMBO J. 16, 7184–7195 (1997)
    Article CAS Google Scholar
  26. Johnson, A. W. Rat1p and Xrn1p are functionally interchangeable exoribonucleases that are restricted to and required in the nucleus and cytoplasm, respectively. Mol. Cell. Biol. 17, 6122–6130 (1997)
    Article CAS Google Scholar
  27. Pinskaya, M. & Morillon, A. Histone H3 lysine 4 di-methylation: a novel mark for transcriptional fidelity? Epigenetics 4, 302–306 (2009)
    Article CAS Google Scholar
  28. Pokholok, D. K. et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517–527 (2005)
    Article CAS Google Scholar
  29. Kirmizis, A. et al. Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation. Nature 449, 928–932 (2007)
    Article ADS CAS Google Scholar
  30. Longtine, M. S. et al. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae . Yeast 14, 953–961 (1998)
    Article CAS Google Scholar
  31. Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression. Bioinformatics 26, 139–140 (2010)
    Article CAS Google Scholar
  32. Dichtl, B., Aasland, R. & Keller, W. Functions for S. cerevisiae Swd2p in 3′ end formation of specific mRNAs and snoRNAs and global histone 3 lysine 4 methylation. RNA 10, 965–977 (2004)
    Article CAS Google Scholar
  33. Pinskaya, M., Gourvennec, S. & Morillon, A. H3 lysine 4 di- and tri-methylation deposited by cryptic transcription attenuates promoter activation. EMBO J. 28, 1697–1707 (2009)
    Article CAS Google Scholar
  34. 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)
    Article CAS Google Scholar
  35. Nonet, M., Scafe, C., Sexton, J. & Young, R. Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol. Cell. Biol. 7, 1602–1611 (1987)
    Article CAS Google Scholar

Download references

Acknowledgements

We thank B. Séraphin, L. Bénard and J. O’Sullivan for support and advice; B. Dichtl for insights into lithium treatment data normalization; M. Wéry and A. Taddei for helpful discussions; A. Johnson, T. Kouzarides and V. Géli for generous gift of plasmids and strains. Special thanks to M. Descrimes, C. Jubin and S. Lair for technical assistance. We thank L. Steinmetz and M. Chodder for sharing unpublished results. E.L.V.D. benefits from an FRM fellowship. This work has benefited from facilities and expertise of the IMAGIF sequencing platform (Centre de Recherche de Gif). This work was financially supported by the Canceropole Ile de France, the ANR “REGULncRNA” and ERC “EPIncRNA” starting grant.

Author information

Author notes

  1. E. L. van Dijk and C. L. Chen: These authors contributed equally to this work.

Authors and Affiliations

  1. Centre de Génétique Moléculaire (CNRS UPR 3404), avenue de la Terrasse, 91198 Gif sur Yvette, France ,
    E. L. van Dijk, C. L. Chen, Y. d’Aubenton-Carafa, M. Silvain, C. Thermes & A. Morillon
  2. ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de recherche, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France ,
    S. Gourvennec, M. Kwapisz, V. Roche, C. Bertrand & A. Morillon
  3. NGS Platform, Institut Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France ,
    P. Legoix-Né
  4. Recombination and Genome instability, Institut Curie, Centre de recherche, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France ,
    S. Loeillet & A. Nicolas

Authors

  1. E. L. van Dijk
  2. C. L. Chen
  3. Y. d’Aubenton-Carafa
  4. S. Gourvennec
  5. M. Kwapisz
  6. V. Roche
  7. C. Bertrand
  8. M. Silvain
  9. P. Legoix-Né
  10. S. Loeillet
  11. A. Nicolas
  12. C. Thermes
  13. A. Morillon

Contributions

E.L.V.D. performed molecular biology experiments, RNA-seq, ChIP-seq libraries and sequencing on the ILLUMINA platform. C.L.C., Y.D.-C., M.S. and C.T. performed statistical and bioinformatic analyses. S.G., M.K., V.R. and C.B. provided technical assistance to molecular biology experiments. A.M., C.T., E.L.V.D. and C.L.C. designed the experiments. P.L.-N. and S.L. performed RNA-seq libraries and NGS sequencing on the SOLiD platform; A.N. managed sequencing on the SOLiD platform. E.L.V.D., C.L.C. and A.N. contributed to the writing. C.T. and A.M. wrote the paper. C.T. and A.M. planned the project.

Corresponding authors

Correspondence toC. Thermes or A. Morillon.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

The file contains Supplementary Figures 1-20 with legends, Supplementary References and Supplementary Tables 1-3. (PDF 1807 kb)

PowerPoint slides

Rights and permissions

About this article

Cite this article

van Dijk, E., Chen, C., d’Aubenton-Carafa, Y. et al. XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast.Nature 475, 114–117 (2011). https://doi.org/10.1038/nature10118

Download citation

This article is cited by

Editorial Summary

Antisense control by ncRNAs

Several lines of evidence suggest that non-coding RNAs (ncRNAs) have a significant role in gene regulation in eukaryotes. Genome-wide deep sequencing in the yeast Saccharomyces cerevisiae has now identified antisense ncRNAs that are destabilized by the Xrn1 RNA exonuclease in the 5′ RNA-decay pathway. These Xrn1-sensitive unstable transcripts, or XUTs, seem to function in gene repression and can be antagonized by histone H3K4 trimethylation.