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Quantifying post-transcriptional regulation in the development of Drosophila melanogaster

Author

Listed:
  • Kolja Becker

    (Institute of Molecular Biology (IMB))

  • Alina Bluhm

    (Institute of Molecular Biology (IMB))

  • Nuria Casas-Vila

    (Institute of Molecular Biology (IMB))

  • Nadja Dinges

    (Institute of Molecular Biology (IMB))

  • Mario Dejung

    (Institute of Molecular Biology (IMB))

  • Sergi Sayols

    (Institute of Molecular Biology (IMB))

  • Clemens Kreutz

    (University of Freiburg)

  • Jean-Yves Roignant

    (Institute of Molecular Biology (IMB))

  • Falk Butter

    (Institute of Molecular Biology (IMB))

  • Stefan Legewie

    (Institute of Molecular Biology (IMB))

Abstract

Even though proteins are produced from mRNA, the correlation between mRNA levels and protein abundances is moderate in most studies, occasionally attributed to complex post-transcriptional regulation. To address this, we generate a paired transcriptome/proteome time course dataset with 14 time points during Drosophila embryogenesis. Despite a limited mRNA-protein correlation (ρ = 0.54), mathematical models describing protein translation and degradation explain 84% of protein time-courses based on the measured mRNA dynamics without assuming complex post transcriptional regulation, and allow for classification of most proteins into four distinct regulatory scenarios. By performing an in-depth characterization of the putatively post-transcriptionally regulated genes, we postulate that the RNA-binding protein Hrb98DE is involved in post-transcriptional control of sugar metabolism in early embryogenesis and partially validate this hypothesis using Hrb98DE knockdown. In summary, we present a systems biology framework for the identification of post-transcriptional gene regulation from large-scale, time-resolved transcriptome and proteome data.

Suggested Citation

  • Kolja Becker & Alina Bluhm & Nuria Casas-Vila & Nadja Dinges & Mario Dejung & Sergi Sayols & Clemens Kreutz & Jean-Yves Roignant & Falk Butter & Stefan Legewie, 2018. "Quantifying post-transcriptional regulation in the development of Drosophila melanogaster," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-07455-9
    DOI: 10.1038/s41467-018-07455-9
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