The long non-coding RNA Cerox1 is a post transcriptional regulator of mitochondrial complex I catalytic activity

Abstract

To generate energy efficiently, the cell is uniquely challenged to co-ordinate the abundance of electron transport chain protein subunits expressed from both nuclear and mitochondrial genomes. How an effective stoichiometry of this many constituent subunits is co-ordinated post-transcriptionally remains poorly understood. Here we show that Cerox1, an unusually abundant cytoplasmic long noncoding RNA (lncRNA), modulates the levels of mitochondrial complex I subunit transcripts in a manner that requires binding to microRNA-488-3p. Increased abundance of Cerox1 cooperatively elevates complex I subunit protein abundance and enzymatic activity, decreases reactive oxygen species production, and protects against the complex I inhibitor rotenone. Cerox1 function is conserved across placental mammals: human and mouse orthologues effectively modulate complex I enzymatic activity in mouse and human cells, respectively. Cerox1 is the first lncRNA demonstrated, to our knowledge, to regulate mitochondrial oxidative phosphorylation and, with miR-488-3p, represent novel targets for the modulation of complex I activity.

Data availability

Microarray data are available through ArrayExpress, accession code E-MATB-6792

The following previously published data sets were used

Article and author information

Author details

  1. Tamara M Sirey

    MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
    For correspondence
    tamara.sirey@igmm.ed.ac.uk
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5606-2858
  2. Kenny Roberts

    MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6155-0821
  3. Wilfried Haerty

    MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
  4. Oscar Bedoya-Reina

    MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    No competing interests declared.
  5. Sebastian Rogatti-Granados

    MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    No competing interests declared.
  6. Jennifer Y Tan

    MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
  7. Nick Li

    MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
  8. Lisa C Heather

    Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
  9. Roderick N Carter

    British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    No competing interests declared.
  10. Sarah Cooper

    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
  11. Andrew J Finch

    MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8065-4623
  12. Jimi Wills

    MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    No competing interests declared.
  13. Nicholas M Morton

    British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, United Kingdom
    Competing interests
    No competing interests declared.
  14. Ana Claudia Marques

    MRC Functional Genomics Unit, University of Oxford, Oxford, United Kingdom
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5174-8092
  15. Chris P Ponting

    MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
    For correspondence
    Chris.Ponting@igmm.ed.ac.uk
    Competing interests
    Chris P Ponting, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0202-7816

Funding

Wellcome (WT106956/Z/15/Z)

  • Tamara M Sirey
  • Oscar Bedoya-Reina
  • Sebastian Rogatti-Granados
  • Chris P Ponting

European Research Council (249869)

  • Tamara M Sirey
  • Kenny Roberts
  • Ana Claudia Marques
  • Chris P Ponting

Wellcome (WT100981/z/13/z)

  • Roderick N Carter
  • Nicholas M Morton

Medical Research Council

  • Wilfried Haerty
  • Chris P Ponting

Diabetes UK

  • Lisa C Heather

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Detlef Weigel, Max Planck Institute for Developmental Biology, Germany

Publication history

  1. Received: January 10, 2019
  2. Accepted: May 2, 2019
  3. Accepted Manuscript published: May 2, 2019 (version 1)
  4. Version of Record published: May 30, 2019 (version 2)
  5. Version of Record updated: August 12, 2019 (version 3)

Copyright

© 2019, Sirey et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Tamara M Sirey
  2. Kenny Roberts
  3. Wilfried Haerty
  4. Oscar Bedoya-Reina
  5. Sebastian Rogatti-Granados
  6. Jennifer Y Tan
  7. Nick Li
  8. Lisa C Heather
  9. Roderick N Carter
  10. Sarah Cooper
  11. Andrew J Finch
  12. Jimi Wills
  13. Nicholas M Morton
  14. Ana Claudia Marques
  15. Chris P Ponting
(2019)
The long non-coding RNA Cerox1 is a post transcriptional regulator of mitochondrial complex I catalytic activity
eLife 8:e45051.
https://doi.org/10.7554/eLife.45051
  1. Further reading

Further reading

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    2. Chromosomes and Gene Expression
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    N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3’end of meiotic mRNAs in both an m6A-dependent and independent manner. Within cells, Pho92 transitions from the nucleus to the cytoplasm, and associates with translating ribosomes. In the nucleus Pho92 associates with target loci through its interaction with transcriptional elongator Paf1C. Functionally, we show that Pho92 promotes and links protein synthesis to mRNA decay. As such, the Pho92-mediated m6A-mRNA decay is contingent on active translation and the CCR4-NOT complex. We propose that the m6A reader Pho92 is loaded co-transcriptionally to facilitate protein synthesis and subsequent decay of m6A modified transcripts, and thereby promotes meiosis.