A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast

  1. Abbas Jariani
  2. Lieselotte Vermeersch
  3. Bram Cerulus
  4. Gemma Perez-Samper
  5. Karin Voordeckers
  6. Thomas Van Brussel
  7. Bernard Thienpont
  8. Diether Lambrechts
  9. Kevin J Verstrepen  Is a corresponding author
  1. VIB-KU Leuven Center for Microbiology, Belgium
  2. VIB-KU Leuven Center for Cancer Biology, Belgium

Abstract

Current methods for single-cell RNA sequencing (scRNA-seq) of yeast cells do not match the throughput and relative simplicity of the state-of-the-art techniques that are available for mammalian cells. In this study, we report how 10x Genomics' droplet-based single-cell RNA sequencing technology can be modified to allow analysis of yeast cells. The protocol, which is based on in-droplet spheroplasting of the cells, yields an order-of-magnitude higher throughput in comparison to existing methods. After extensive validation of the method, we demonstrate its use by studying the dynamics of the response of isogenic yeast populations to a shift in carbon source, revealing the heterogeneity and underlying molecular processes during this shift. The method we describe opens new avenues for studies focusing on yeast cells, as well as other cells with a degradable cell wall.

Data availability

Sequencing data have been deposited in GEO under accession code GSE144820

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

Article and author information

Author details

  1. Abbas Jariani

    VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2715-933X
  2. Lieselotte Vermeersch

    VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5789-2220
  3. Bram Cerulus

    VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
    Competing interests
    No competing interests declared.
  4. Gemma Perez-Samper

    VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
    Competing interests
    No competing interests declared.
  5. Karin Voordeckers

    VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
    Competing interests
    No competing interests declared.
  6. Thomas Van Brussel

    VIB-KU Leuven Laboratory for Translational Genetics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
    Competing interests
    No competing interests declared.
  7. Bernard Thienpont

    VIB-KU Leuven Laboratory for Translational Genetics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8772-6845
  8. Diether Lambrechts

    VIB-KU Leuven Laboratory for Translational Genetics, VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
    Competing interests
    No competing interests declared.
  9. Kevin J Verstrepen

    VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, Belgium
    For correspondence
    kevin.verstrepen@kuleuven.vib.be
    Competing interests
    Kevin J Verstrepen, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3077-6219

Funding

Fonds Wetenschappelijk Onderzoek

  • Lieselotte Vermeersch
  • Bram Cerulus

Vlaams Instituut voor Biotechnologie

  • Kevin J Verstrepen

European Research Council (Council CoG682009)

  • Kevin J Verstrepen

AB-InBev-Baillet Latour Fund

  • Kevin J Verstrepen

Human Frontier Science Program (246 RGP0050/2013)

  • Kevin J Verstrepen

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

Reviewing Editor

  1. Antonis Rokas, Vanderbilt University, United States

Version history

  1. Received: January 20, 2020
  2. Accepted: May 15, 2020
  3. Accepted Manuscript published: May 18, 2020 (version 1)
  4. Version of Record published: May 29, 2020 (version 2)

Copyright

© 2020, Jariani 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. Abbas Jariani
  2. Lieselotte Vermeersch
  3. Bram Cerulus
  4. Gemma Perez-Samper
  5. Karin Voordeckers
  6. Thomas Van Brussel
  7. Bernard Thienpont
  8. Diether Lambrechts
  9. Kevin J Verstrepen
(2020)
A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast
eLife 9:e55320.
https://doi.org/10.7554/eLife.55320

Share this article

https://doi.org/10.7554/eLife.55320

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