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TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway

Nature Structural & Molecular Biology volume 15, pages 1015–1023 (2008)Cite this article

Abstract

In the fission yeast Schizosaccharomyces pombe, the RNA interference (RNAi) machinery is required to generate small interfering RNAs (siRNAs) that mediate heterochromatic gene silencing. Efficient silencing also requires the TRAMP complex, which contains the noncanonical Cid14 poly(A) polymerase and targets aberrant RNAs for degradation. Here we use high-throughput sequencing to analyze Argonaute-associated small RNAs (sRNAs) in both the presence and absence of Cid14. Most sRNAs in fission yeast start with a 5′ uracil, and we argue these are loaded most efficiently into Argonaute. In wild-type cells most sRNAs match to repeated regions of the genome, whereas in cid14Δ cells the sRNA profile changes to include major new classes of sRNAs originating from ribosomal RNAs and a tRNA. Thus, Cid14 prevents certain abundant RNAs from becoming substrates for the RNAi machinery, thereby freeing the RNAi machinery to act on its proper targets.

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Figure 1: Profiling of Ago1-associated small RNAs from wild-type cells.
Figure 2: Distribution of reads mapping to genomic loci.
Figure 3: Profiling of Ago1-associated small RNAs from cid14Δ cells.
Figure 4: Small RNAs generated from centromeres in wild-type and cid14Δ cells.
Figure 5: Ribosomal RNAs give rise to antisense siRNAs (rr-siRNAs) in cid14Δ cells.
Figure 6: Model for competition between the RNAi and the Cid14–TRAMP RNA surveillance pathways.

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Acknowledgements

We thank W. Johnston and S. Buker for reagents and members of the Moazed and Bartel laboratories for helpful discussions. We also thank H. Grosshans for comments on the manuscript. M.B. was supported by a Swiss National Science Foundation postdoctoral fellowship and is currently supported by the Novartis Research Foundation and the Swiss National Science Foundation SNF Professorship. This work was supported by grants from the US National Institutes of Health (D.M.) and the Howard Hughes Medical Institute (D.P.B.).

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  1. Marc Bühler

    Present address: Present address: Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,

  2. Marc Bühler and Noah Spies: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Marc Bühler & Danesh Moazed

  2. Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology and Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, 02142, Massachusetts, USA

    Noah Spies & David P Bartel

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  1. Marc Bühler
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Contributions

M.B. performed the experimental work with yeast; N.S. performed the computational analysis of sequencing reads; All authors contributed to the design of the study and preparation of the manuscript.

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Correspondence to David P Bartel or Danesh Moazed.

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Bühler, M., Spies, N., Bartel, D. et al. TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat Struct Mol Biol 15, 1015–1023 (2008). https://doi.org/10.1038/nsmb.1481

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