Transcriptome maps of general eukaryotic RNA degradation factors

Abstract

RNA degradation pathways enable RNA processing, the regulation of RNA levels, and the surveillance of aberrant or poorly functional RNAs in cells. Here we provide transcriptome-wide RNA-binding profiles of 30 general RNA degradation factors in the yeast Saccharomyces cerevisiae. The profiles reveal the distribution of degradation factors between different RNA classes. They are consistent with the canonical degradation pathway for closed-loop forming mRNAs after deadenylation. Modeling based on mRNA half-lives suggests that most degradation factors bind intact mRNAs, whereas decapping factors are recruited only for mRNA degradation, consistent with decapping being a rate-limiting step. Decapping factors preferentially bind mRNAs with non-optimal codons, consistent with rapid degradation of inefficiently translated mRNAs. Global analysis suggests that the nuclear surveillance machinery, including the complexes Nrd1/Nab3 and TRAMP4, targets aberrant nuclear RNAs and processes snoRNAs.

Data availability

Sequencing data have been deposited in GEO under accession codes GSE 128312.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Salma Sohrabi-Jahromi

    Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8417-8230
  2. Katharina B Hofmann

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0683-6277
  3. Andrea Boltendahl

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  4. Christian Roth

    Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  5. Saskia Gressel

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0261-675X
  6. Carlo Baejen

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  7. Johannes Soeding

    Quantitative and Computational Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
    For correspondence
    johannes.soeding@mpibpc.mpg.de
    Competing interests
    The authors declare that no competing interests exist.
  8. Patrick Cramer

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
    For correspondence
    patrick.cramer@mpibpc.mpg.de
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5454-7755

Funding

European Research Council (Advanced Grant Transregulon)

  • Patrick Cramer

Volkswagen Foundation

  • Patrick Cramer

Deutsche Forschungsgemeinschaft (SPP1935 grant CR 117/6-1)

  • Johannes Soeding
  • Patrick Cramer

Max-Planck-Gesellschaft (Open-Access funding)

  • Patrick Cramer

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

Reviewing Editor

  1. Torben Heick Jensen, Aarhus University, Denmark

Publication history

  1. Received: March 24, 2019
  2. Accepted: May 27, 2019
  3. Accepted Manuscript published: May 28, 2019 (version 1)
  4. Version of Record published: June 14, 2019 (version 2)

Copyright

© 2019, Sohrabi-Jahromi 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. Salma Sohrabi-Jahromi
  2. Katharina B Hofmann
  3. Andrea Boltendahl
  4. Christian Roth
  5. Saskia Gressel
  6. Carlo Baejen
  7. Johannes Soeding
  8. Patrick Cramer
(2019)
Transcriptome maps of general eukaryotic RNA degradation factors
eLife 8:e47040.
https://doi.org/10.7554/eLife.47040
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