Abstract

Nuclear processing and quality control of eukaryotic RNA is mediated by the RNA exosome, which is regulated by accessory factors. However, the mechanism of exosome recruitment to its ribonucleoprotein (RNP) targets remains poorly understood. Here we report a physical link between the human exosome and the cap-binding complex (CBC). The CBC associates with the ARS2 protein to form CBC–ARS2 (CBCA) and then further connects, together with the ZC3H18 protein, to the nuclear exosome targeting (NEXT) complex, thus forming CBC–NEXT (CBCN). RNA immunoprecipitation using CBCN factors as well as the analysis of combinatorial depletion of CBCN and exosome components underscore the functional relevance of CBC-exosome bridging at the level of target RNA. Specifically, CBCA suppresses read-through products of several RNA families by promoting their transcriptional termination. We suggest that the RNP 5′ cap links transcription termination to exosomal RNA degradation through CBCN.

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Acknowledgements

We thank M. Schmid, S. Lykke-Andersen, M. Lubas, A. Dziembowski and D. Libri for critical comments to the manuscript. Special thanks go to E. Marchal for excellent technical assistance. E. Izaurralde (Max Planck Institute for Developmental Biology) and J. Lykke-Andersen (Division of Biological Sciences at University of California, San Diego) are acknowledged for sharing reagents. This work was supported by the Danish National Research Foundation (grant DNRF58), the Danish Cancer Society and the Lundbeck and Novo Nordisk Foundations (T.H.J.); the US National Institutes of Health (grant U54 GM103511, to M.P.R.), the l'ARC and La Ligue Contre Le Cancer (E.B.), the Foundation for Strategic Research (grant FFL09-0130, to R.S.) and the European Community's Seventh Framework Programme (FP7/2007-2013) under grant no. 241548 (MitoSys, to A.H.).

Author information

Author notes

    • Maiken S Kristiansen
    •  & Aleks Schein

    Present addresses: Sir William Dunn School of Pathology, University of Oxford, Oxford, UK (M.S.K.), and Division of Genomic Technologies, RIKEN, Yokohama City, Japan (A.S.).

    • Peter Refsing Andersen
    •  & Michal Domanski

    These authors contributed equally to this work.

Affiliations

  1. Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.

    • Peter Refsing Andersen
    • , Michal Domanski
    • , Maiken S Kristiansen
    • , Evgenia Ntini
    • , Aleks Schein
    •  & Torben Heick Jensen
  2. Laboratory of Cellular and Structural Biology, Rockefeller University, New York, New York, USA.

    • Michal Domanski
    • , John LaCava
    •  & Michael P Rout
  3. Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.

    • Helena Storvall
    •  & Rickard Sandberg
  4. Institute de Génétique Moléculaire Montpellier, CNRS, Montpellier, France.

    • Celine Verheggen
    • , Marie Hallais
    •  & Edouard Bertrand
  5. Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.

    • Jakob Bunkenborg
    •  & Jens S Andersen
  6. Max Planck Institute of Molecular Biology & Genetics, Dresden, Germany.

    • Ina Poser
    •  & Anthony Hyman

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Contributions

M.D. and J.B. performed ACMS experiments and analyzed the data together with J.S.A., J.L. and M.P.R.; I.P. and A.H. contributed tagged cell lines. C.V., M.H. and E.B. performed and analyzed RIP experiments. P.R.A., M.S.K. and A.S. performed experimental RNA analyses. P.R.A. and E.N. performed and analyzed ChIP experiments. P.R.A., H.S. and R.S. analyzed RNA-seq data. P.R.A., M.D., M.S.K. and T.H.J. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Torben Heick Jensen.

Integrated supplementary information

Supplementary information

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  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–6, Supplementary Tables 1 and 8–13 and Supplementary Note

Excel files

  1. 1.

    Supplementary Table 2

    hMTR4-LAP ACMS

  2. 2.

    Supplementary Table 3

    RBM7-LAP ACMS

  3. 3.

    Supplementary Table 4

    CBP80–3× FLAG ACMS

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    Supplementary Table 5

    CBP20–3× FLAG ACMS

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    Supplementary Table 6

    LAP-ARS2 ACMS

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    Supplementary Table 7

    ZC3H18–3× FLAG ACMS

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DOI

https://doi.org/10.1038/nsmb.2703

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