Generation of a versatile BiFC ORFeome library for analyzing protein-protein interactions in live Drosophila

  1. Johannes Bischof
  2. Marilyne Duffraisse
  3. Edy Furger
  4. Leiore Ajuria
  5. Guillaume Giraud
  6. Solene Vanderperre
  7. Rachel Paul
  8. Mikael Björklund
  9. Damien Ahr
  10. Alexis W Ahmed
  11. Lionel Spinelli
  12. Christine Brun
  13. Konrad Basler
  14. Samir Merabet  Is a corresponding author
  1. University of Zurich, Switzerland
  2. Institut de Génomique Fonctionnelle de Lyon, France
  3. Zhejiang University, China
  4. Aix Marseille University, France

Abstract

Transcription factors achieve specificity by establishing intricate interaction networks that will change depending on the cell context. Capturing these interactions in live condition is however a challenging issue that requires sensitive and non-invasive methods. We present a set of fly lines, called 'multicolor BiFC library', which covers most of the Drosophila transcription factors for performing Bimolecular Fluorescence Complementation (BiFC). The multicolor BiFC library can be used to probe two different binary interactions simultaneously and is compatible for large-scale interaction screens. The library can also be coupled with established Drosophila genetic resources to analyze interactions in the developmentally relevant expression domain of each protein partner. We provide proof of principle experiments of these various applications, using Hox proteins in the live Drosophila embryo as a case study. Overall this novel collection of ready-to-use fly lines constitutes an unprecedented genetic toolbox for the identification and analysis of protein-protein interactions in vivo.

Data availability

Fly lines generated for the project have been deposited to the FlyORF library and are available upon request to FlyORF (https://flyorf.ch/index.php/orf-collection). The numerical, processed data used for this study is provided in the manuscript, figures and supplementary files.

Article and author information

Author details

  1. Johannes Bischof

    Institute of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
    Competing interests
    Johannes Bischof, involved in maintaining and distributing the fly lines via the not-for-profit FlyORF project. There are no other competing interests to declare.
  2. Marilyne Duffraisse

    ENS Lyon UMR5242, Institut de Génomique Fonctionnelle de Lyon, Lyon, France
    Competing interests
    No competing interests declared.
  3. Edy Furger

    Institute of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
    Competing interests
    No competing interests declared.
  4. Leiore Ajuria

    ENS Lyon UMR5242, Institut de Génomique Fonctionnelle de Lyon, Lyon, France
    Competing interests
    No competing interests declared.
  5. Guillaume Giraud

    ENS Lyon UMR5242, Institut de Génomique Fonctionnelle de Lyon, Lyon, France
    Competing interests
    No competing interests declared.
  6. Solene Vanderperre

    ENS Lyon UMR5242, Institut de Génomique Fonctionnelle de Lyon, Lyon, France
    Competing interests
    No competing interests declared.
  7. Rachel Paul

    ENS Lyon UMR5242, Institut de Génomique Fonctionnelle de Lyon, Lyon, France
    Competing interests
    No competing interests declared.
  8. Mikael Björklund

    Zhejiang University-University of Edinburgh Institute, Zhejiang University, Haining, China
    Competing interests
    Mikael Björklund, involved in the development of the FlyORF resource. There are no other competing interests to declare.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2176-681X
  9. Damien Ahr

    ENS Lyon UMR5242, Institut de Génomique Fonctionnelle de Lyon, Lyon, France
    Competing interests
    No competing interests declared.
  10. Alexis W Ahmed

    ENS Lyon UMR5242, Institut de Génomique Fonctionnelle de Lyon, Lyon, France
    Competing interests
    No competing interests declared.
  11. Lionel Spinelli

    TAGC U1090, Aix Marseille University, Marseille, France
    Competing interests
    No competing interests declared.
  12. Christine Brun

    TAGC U1090, Aix Marseille University, Marseille, France
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5563-6765
  13. Konrad Basler

    Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
    Competing interests
    Konrad Basler, involved in maintaining and distributing the fly lines via the not-for-profit FlyORF project. There are no other competing interests to declare.
  14. Samir Merabet

    ENS Lyon UMR5242, Institut de Génomique Fonctionnelle de Lyon, Lyon, France
    For correspondence
    samir.merabet@ens-lyon.fr
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7629-703X

Funding

Fondation pour la Recherche Médicale (1122556)

  • Johannes Bischof
  • Marilyne Duffraisse
  • Edy Furger
  • Leiore Ajuria
  • Guillaume Giraud
  • Solene Vanderperre
  • Rachel Paul
  • Samir Merabet

Cefipra

  • Johannes Bischof
  • Marilyne Duffraisse
  • Edy Furger
  • Leiore Ajuria
  • Guillaume Giraud
  • Solene Vanderperre
  • Rachel Paul
  • Samir Merabet

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

Reviewing Editor

  1. K VijayRaghavan, National Centre for Biological Sciences, Tata Institute of Fundamental Research, India

Publication history

  1. Received: June 1, 2018
  2. Accepted: September 18, 2018
  3. Accepted Manuscript published: September 24, 2018 (version 1)
  4. Version of Record published: October 9, 2018 (version 2)

Copyright

© 2018, Bischof 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.

Metrics

  • 4,904
    Page views
  • 775
    Downloads
  • 23
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Johannes Bischof
  2. Marilyne Duffraisse
  3. Edy Furger
  4. Leiore Ajuria
  5. Guillaume Giraud
  6. Solene Vanderperre
  7. Rachel Paul
  8. Mikael Björklund
  9. Damien Ahr
  10. Alexis W Ahmed
  11. Lionel Spinelli
  12. Christine Brun
  13. Konrad Basler
  14. Samir Merabet
(2018)
Generation of a versatile BiFC ORFeome library for analyzing protein-protein interactions in live Drosophila
eLife 7:e38853.
https://doi.org/10.7554/eLife.38853

Further reading

    1. Evolutionary Biology
    2. Genetics and Genomics
    Khai C Ang, Victor A Canfield ... Keith C Cheng
    Research Article

    Our interest in the genetic basis of skin color variation between populations led us to seek a Native American population with genetically African admixture but low frequency of European light skin alleles. Analysis of 458 genomes from individuals residing in the Kalinago territory of the Commonwealth of Dominica showed approximately 55% Native American, 32% African, and 12% European genetic ancestry, the highest Native American genetic ancestry among Caribbean populations to date. Skin pigmentation ranged from 20 to 80 melanin units, averaging 46. Three albino individuals were determined to be homozygous for a causative multi-nucleotide polymorphism OCA2NW273KV contained within a haplotype of African origin; its allele frequency was 0.03 and single allele effect size was -8 melanin units. Derived allele frequencies of SLC24A5A111T and SLC45A2L374F were 0.14 and 0.06, with single allele effect sizes of -6 and -4, respectively. Native American genetic ancestry by itself reduced pigmentation by more than 20 melanin units (range 24 - 29). The responsible hypopigmenting genetic variants remain to be identified, since none of the published polymorphisms predicted in prior literature to affect skin color in Native Americans caused detectable hypopigmentation in the Kalinago.

    1. Genetics and Genomics
    Gemma E May, Christina Akirtava ... Joel McManus
    Research Article Updated

    Upstream open-reading frames (uORFs) are potent cis-acting regulators of mRNA translation and nonsense-mediated decay (NMD). While both AUG- and non-AUG initiated uORFs are ubiquitous in ribosome profiling studies, few uORFs have been experimentally tested. Consequently, the relative influences of sequence, structural, and positional features on uORF activity have not been determined. We quantified thousands of yeast uORFs using massively parallel reporter assays in wildtype and ∆upf1 yeast. While nearly all AUG uORFs were robust repressors, most non-AUG uORFs had relatively weak impacts on expression. Machine learning regression modeling revealed that both uORF sequences and locations within transcript leaders predict their effect on gene expression. Indeed, alternative transcription start sites highly influenced uORF activity. These results define the scope of natural uORF activity, identify features associated with translational repression and NMD, and suggest that the locations of uORFs in transcript leaders are nearly as predictive as uORF sequences.