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Nuclear stability and transcriptional directionality separate functionally distinct RNA species

Author

Listed:
  • Robin Andersson

    (The Bioinformatics Centre, University of Copenhagen)

  • Peter Refsing Andersen

    (Centre for mRNP Biogenesis and Metabolism
    Present address: Department of Hematology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark)

  • Eivind Valen

    (University of Bergen
    Harvard University)

  • Leighton J. Core

    (Cornell University
    Institute for Systems Genomics, University of Connecticut)

  • Jette Bornholdt

    (The Bioinformatics Centre, University of Copenhagen)

  • Mette Boyd

    (The Bioinformatics Centre, University of Copenhagen)

  • Torben Heick Jensen

    (Centre for mRNP Biogenesis and Metabolism)

  • Albin Sandelin

    (The Bioinformatics Centre, University of Copenhagen)

Abstract

Mammalian genomes are pervasively transcribed, yielding a complex transcriptome with high variability in composition and cellular abundance. Although recent efforts have identified thousands of new long non-coding (lnc) RNAs and demonstrated a complex transcriptional repertoire produced by protein-coding (pc) genes, limited progress has been made in distinguishing functional RNA from spurious transcription events. This is partly due to present RNA classification, which is typically based on technical rather than biochemical criteria. Here we devise a strategy to systematically categorize human RNAs by their sensitivity to the ribonucleolytic RNA exosome complex and by the nature of their transcription initiation. These measures are surprisingly effective at correctly classifying annotated transcripts, including lncRNAs of known function. The approach also identifies uncharacterized stable lncRNAs, hidden among a vast majority of unstable transcripts. The predictive power of the approach promises to streamline the functional analysis of known and novel RNAs.

Suggested Citation

  • Robin Andersson & Peter Refsing Andersen & Eivind Valen & Leighton J. Core & Jette Bornholdt & Mette Boyd & Torben Heick Jensen & Albin Sandelin, 2014. "Nuclear stability and transcriptional directionality separate functionally distinct RNA species," Nature Communications, Nature, vol. 5(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms6336
    DOI: 10.1038/ncomms6336
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    Cited by:

    1. Irene Robles-Rebollo & Sergi Cuartero & Adria Canellas-Socias & Sarah Wells & Mohammad M. Karimi & Elisabetta Mereu & Alexandra G. Chivu & Holger Heyn & Chad Whilding & Dirk Dormann & Samuel Marguerat, 2022. "Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Xavier Contreras & David Depierre & Charbel Akkawi & Marina Srbic & Marion Helsmoortel & Maguelone Nogaret & Matthieu LeHars & Kader Salifou & Alexandre Heurteau & Olivier Cuvier & Rosemary Kiernan, 2023. "PAPĪ³ associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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