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Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping

Abstract

We have determined the high-resolution strand-specific transcriptome of the fission yeast S. pombe under multiple growth conditions using a novel RNA-DNA hybridization mapping (HybMap) technique. HybMap uses an antibody against an RNA-DNA hybrid to detect RNA molecules hybridized to a high-density DNA oligonucleotide tiling microarray. HybMap showed exceptional dynamic range and reproducibility, and allowed us to identify strand-specific coding, noncoding and structural RNAs, as well as previously unknown RNAs conserved in distant yeast species. Notably, we found that virtually the entire euchromatic genome (including intergenics) is transcribed, with heterochromatin dampening intergenic transcription. We identified features including large numbers of condition-specific noncoding RNAs, extensive antisense transcription, new properties of antisense transcripts and induced divergent transcription. Furthermore, our HybMap data informed the efficiency and locations of RNA splicing genome-wide. Finally, we observed strand-specific transcription islands around tRNAs at heterochromatin boundaries inside centromeres. Here, we discuss these new features in terms of organism fitness and transcriptome evolution.

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Figure 1: Extensive transcription of the S. pombe genome.
Figure 2: Features of transcription and splicing in euchromatin.
Figure 3: Quantitation of transcription fragments and potential noncoding RNAs.
Figure 4: Transcriptomes and loci derived from alternative growth conditions.
Figure 5: Features of antisense transcription.
Figure 6: Poly(A) RNA shows divergent transcription and previously unknown RNA transcripts.
Figure 7: Transcriptional features of heterochromatic loci and flanking regions.

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References

  1. Birney, E. et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007).

    CAS  Article  PubMed  Google Scholar 

  2. Okazaki, Y. et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563–573 (2002).

    Article  PubMed  Google Scholar 

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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  4. Washietl, S., Hofacker, I.L., Lukasser, M., Huttenhofer, A. & Stadler, P.F. Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat. Biotechnol. 23, 1383–1390 (2005).

    CAS  Article  PubMed  Google Scholar 

  5. Kampa, D. et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res. 14, 331–342 (2004).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  6. Steigele, S., Huber, W., Stocsits, C., Stadler, P.F. & Nieselt, K. Comparative analysis of structured RNAs in S. cerevisiae indicates a multitude of different functions. BMC Biol. 5, 25 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

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

    CAS  Article  PubMed  Google Scholar 

  8. Perocchi, F., Xu, Z., Clauder-Munster, S. & Steinmetz, L.M. Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucleic Acids Res. 35, e128 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  9. Hu, Z., Zhang, A., Storz, G., Gottesman, S. & Leppla, S.H. An antibody-based microarray assay for small RNA detection. Nucleic Acids Res. 34, e52 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  10. Boguslawski, S.J. et al. Characterization of monoclonal antibody to DNA.RNA and its application to immunodetection of hybrids. J. Immunol. Methods 89, 123–130 (1986).

    CAS  Article  PubMed  Google Scholar 

  11. Kapranov, P., Willingham, A.T. & Gingeras, T.R. Genome-wide transcription and the implications for genomic organization. Nat. Rev. Genet. 8, 413–423 (2007).

    CAS  Article  PubMed  Google Scholar 

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

    CAS  Article  PubMed  Google Scholar 

  13. Wood, V. et al. The genome sequence of Schizosaccharomyces pombe. Nature 415, 871–880 (2002).

    CAS  Article  PubMed  Google Scholar 

  14. Leonardi, J., Box, J.A., Bunch, J.T. & Baumann, P. TER1, the RNA subunit of fission yeast telomerase. Nat. Struct. Mol. Biol. 15, 26–33 (2008).

    CAS  Article  PubMed  Google Scholar 

  15. Webb, C.J. & Zakian, V.A. Identification and characterization of the Schizosaccharomyces pombe TER1 telomerase RNA. Nat. Struct. Mol. Biol. 15, 34–42 (2008).

    CAS  Article  PubMed  Google Scholar 

  16. Gordon, M. et al. Genome-wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries. Mol. Cell. Biol. 27, 4058–4069 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  17. Chen, D. et al. Global transcriptional responses of fission yeast to environmental stress. Mol. Biol. Cell 14, 214–229 (2003).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  18. Katayama, S. et al. Antisense transcription in the mammalian transcriptome. Science 309, 1564–1566 (2005).

    Article  PubMed  Google Scholar 

  19. Nicolas, E. et al. Distinct roles of HDAC complexes in promoter silencing, antisense suppression and DNA damage protection. Nat. Struct. Mol. Biol. 14, 372–380 (2007).

    CAS  Article  PubMed  Google Scholar 

  20. Wiren, M. et al. Genomewide analysis of nucleosome density histone acetylation and HDAC function in fission yeast. EMBO J. 24, 2906–2918 (2005).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  21. Noma, K., Cam, H.P., Maraia, R.J. & Grewal, S.I. A role for TFIIIC transcription factor complex in genome organization. Cell 125, 859–872 (2006).

    CAS  Article  PubMed  Google Scholar 

  22. Volpe, T.A. et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833–1837 (2002).

    CAS  Article  PubMed  Google Scholar 

  23. Allshire, R.C., Javerzat, J.P., Redhead, N.J. & Cranston, G. Position effect variegation at fission yeast centromeres. Cell 76, 157–169 (1994).

    CAS  Article  PubMed  Google Scholar 

  24. Takahashi, K. et al. A low copy number central sequence with strict symmetry and unusual chromatin structure in fission yeast centromere. Mol. Biol. Cell 3, 819–835 (1992).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  25. Scott, K.C., White, C.V. & Willard, H.F. An RNA polymerase III-dependent heterochromatin barrier at fission yeast centromere 1. PLoS ONE 2, e1099 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  26. Baum, M., Ngan, V.K. & Clarke, L. The centromeric K-type repeat and the central core are together sufficient to establish a functional Schizosaccharomyces pombe centromere. Mol. Biol. Cell 5, 747–761 (1994).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  27. Partridge, J.F., Scott, K.S., Bannister, A.J., Kouzarides, T. & Allshire, R.C. cis-acting DNA from fission yeast centromeres mediates histone H3 methylation and recruitment of silencing factors and cohesin to an ectopic site. Curr. Biol. 12, 1652–1660 (2002).

    CAS  Article  PubMed  Google Scholar 

  28. Steiner, N.C., Hahnenberger, K.M. & Clarke, L. Centromeres of the fission yeast Schizosaccharomyces pombe are highly variable genetic loci. Mol. Cell. Biol. 13, 4578–4587 (1993).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  29. Clarke, L., Amstutz, H., Fishel, B. & Carbon, J. Analysis of centromeric DNA in the fission yeast Schizosaccharomyces pombe. Proc. Natl. Acad. Sci. USA 83, 8253–8257 (1986).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  30. Nakaseko, Y., Kinoshita, N. & Yanagida, M. A novel sequence common to the centromere regions of Schizosaccharomyces pombe chromosomes. Nucleic Acids Res. 15, 4705–4715 (1987).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  31. Nakaseko, Y., Adachi, Y., Funahashi, S., Niwa, O. & Yanagida, M. Chromosome walking shows a highly homologous repetitive sequence present in all the centromere regions of fission yeast. EMBO J. 5, 1011–1021 (1986).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  32. Motamedi, M.R. et al. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119, 789–802 (2004).

    CAS  Article  PubMed  Google Scholar 

  33. Lindsey-Boltz, L.A. & Sancar, A. RNA polymerase: the most specific damage recognition protein in cellular responses to DNA damage? Proc. Natl. Acad. Sci. USA 104, 13213–13214 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. Cam, H.P. et al. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat. Genet. 37, 809–819 (2005).

    CAS  Article  PubMed  Google Scholar 

  35. Verdel, A. et al. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303, 672–676 (2004).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  36. Reinhart, B.J. & Bartel, D.P. Small RNAs correspond to centromere heterochromatic repeats. Science 297, 1831 (2002).

    CAS  Article  PubMed  Google Scholar 

  37. Kato, H. et al. RNA polymerase II is required for RNAi-dependent heterochromatin assembly. Science 309, 467–469 (2005).

    CAS  Article  PubMed  Google Scholar 

  38. Bolstad, B.M., Irizarry, R.A., Astrand, M. & Speed, T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185–193 (2003).

    CAS  Article  PubMed  Google Scholar 

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Acknowledgements

We thank S. Leppla (US National Institutes of Health) for generously providing the S9.6 antibody and Bob Schackmann (University of Utah) for oligo synthesis. The work was supported by the Howard Hughes Medical Institute (B.R.C., D.H., T.J.P., and supplies), US National Institutes of Health Genetics Training Grant T32 GM007464 (N.D.), the Huntsman Cancer Institute (D.A.N.), and CA24014 (for core facilities).

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Contributions

N.D., D.A.N., and B.R.C.; system design and experimental approaches. B.D.; array method optimization. D.A.N., N.D., B.M., T.J.P., D.H., and B.R.C.; array design, data analysis methods and data analysis. E.W.; feature computation. N.D., D.A.N., and D.H.; figures. B.R.C., N.D. and D.A.N. wrote the manuscript.

Corresponding author

Correspondence to Bradley R Cairns.

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Supplementary Figures 1–9, Supplementary Tables 1–11, Supplementary Note, Supplementary Methods (PDF 1308 kb)

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Dutrow, N., Nix, D., Holt, D. et al. Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping. Nat Genet 40, 977–986 (2008). https://doi.org/10.1038/ng.196

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