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

Nature Genetics volume 40, pages 977–986 (2008)Cite this article

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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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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Authors and Affiliations

  1. Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, 84132, Utah, USA

    Natalie Dutrow, Derick Holt, Erick Westbroek, Timothy J Parnell & Bradley R Cairns

  2. Howard Hughes Medical Institute and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, 84112, Utah, USA

    Natalie Dutrow, Derick Holt, Erick Westbroek, Timothy J Parnell & Bradley R Cairns

  3. Research Informatics, Huntsman Cancer Institute, Salt Lake City, 84112, USA

    David A Nix

  4. Bioinformatics Core Facility, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, 84112, USA

    David A Nix & Brett Milash

  5. Microarray Core Facility, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, 84112, USA

    Brian Dalley

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  1. Natalie Dutrow
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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.

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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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