Quantifying post-transcriptional regulation in the development of Drosophila melanogaster

Kolja Becker, Alina Bluhm, Nuria Casas-Vila, Nadja Dinges, Mario Dejung, Sergi Sayols, Clemens Kreutz, Jean-Yves Roignant, Falk Butter () and Stefan Legewie ()
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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)

Nature Communications, 2018, vol. 9, issue 1, 1-14

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-07455-9

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