Topology-driven protein-protein interaction network analysis detects genetic sub-networks regulating reproductive capacity

  1. Tarun Kumar
  2. Leo Blondel
  3. Cassandra G Extavour  Is a corresponding author
  1. Harvard University, United States

Abstract

Understanding the genetic regulation of organ structure is a fundamental problem in developmental biology. Here, we use egg-producing structures of insect ovaries, called ovarioles, to deduce systems-level gene regulatory relationships from quantitative functional genetic analysis. We previously showed that Hippo signalling, a conserved regulator of animal organ size, regulates ovariole number in Drosophila melanogaster. To comprehensively determine how Hippo signalling interacts with other pathways in this regulation, we screened all known signalling pathway genes, and identified Hpo-dependent and Hpo-independent signalling requirements. Network analysis of known protein-protein interactions among screen results identified independent gene regulatory sub-networks regulating one or both of ovariole number and egg laying. These sub-networks predict involvement of previously uncharacterised genes with higher accuracy than the original candidate screen. This shows that network analysis combining functional genetic and large-scale interaction data can predict function of novel genes regulating development.

Data availability

This study did not generate new unique reagents. This study generated new python3 code available on GitHub: https://github.com/extavourlab/hpo_ova_eggL_screen.

Article and author information

Author details

  1. Tarun Kumar

    Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4071-4342
  2. Leo Blondel

    Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2276-4821
  3. Cassandra G Extavour

    Department of Organismic and Evolutionary Biology/Molecular and Cellular Biology, Harvard University, Cambridge, United States
    For correspondence
    extavour@oeb.harvard.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2922-5855

Funding

National Institutes of Health (1R01-HD073499)

  • Tarun Kumar
  • Cassandra G Extavour

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

Reviewing Editor

  1. Michael B Eisen, University of California, Berkeley, United States

Version history

  1. Received: December 1, 2019
  2. Accepted: September 1, 2020
  3. Accepted Manuscript published: September 9, 2020 (version 1)
  4. Version of Record published: October 12, 2020 (version 2)

Copyright

© 2020, Kumar 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. Tarun Kumar
  2. Leo Blondel
  3. Cassandra G Extavour
(2020)
Topology-driven protein-protein interaction network analysis detects genetic sub-networks regulating reproductive capacity
eLife 9:e54082.
https://doi.org/10.7554/eLife.54082

Share this article

https://doi.org/10.7554/eLife.54082

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