A precisely adjustable, variation-suppressed eukaryotic transcriptional controller to enable genetic discovery

  1. Asli Azizoglu  Is a corresponding author
  2. Roger Brent  Is a corresponding author
  3. Fabian Rudolf  Is a corresponding author
  1. ETH Zurich, Switzerland
  2. Fred Hutchinson Cancer Research Center, United States

Abstract

Conditional expression of genes and observation of phenotype remain central to biological discovery. Current methods enable either on/off or imprecisely controlled graded gene expression. We developed a 'well-tempered' controller, WTC846, for precisely adjustable, graded, growth condition independent expression of genes in Saccharomyces cerevisiae. Controlled genes are expressed from a strong semisynthetic promoter repressed by the prokaryotic TetR, which also represses its own synthesis; with basal expression abolished by a second, 'zeroing' repressor. The autorepression loop lowers cell-to-cell variation while enabling precise adjustment of protein expression by a chemical inducer. WTC846 allelic strains in which the controller replaced the native promoters recapitulated known null phenotypes (CDC42, TPI1), exhibited novel overexpression phenotypes (IPL1), showed protein dosage-dependent growth rates and morphological phenotypes (CDC28, TOR2, PMA1 and the hitherto uncharacterized PBR1), and enabled cell cycle synchronization (CDC20). WTC846 defines an 'expression clamp' allowing protein dosage to be adjusted by the experimenter across the range of cellular protein abundances, with limited variation around the setpoint.

Data availability

All relevant sequences are included in the supporting files for reproducibility. All raw flow cytometry data is publicly available at doi.org/10.3929/ethz-b-000488967. All other source data is included in the manuscript and supporting files.

Article and author information

Author details

  1. Asli Azizoglu

    BSSE, ETH Zurich, Basel, Switzerland
    For correspondence
    asli.azizoglu@bsse.ethz.ch
    Competing interests
    The authors declare that no competing interests exist.
  2. Roger Brent

    Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
    For correspondence
    rbrent@fhcrc.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8398-3273
  3. Fabian Rudolf

    D-BSSE, ETH Zurich, Basel, Switzerland
    For correspondence
    fabian.rudolf@bsse.ethz.ch
    Competing interests
    The authors declare that no competing interests exist.

Funding

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (NCCR Molecular Systems Engineering)

  • Asli Azizoglu
  • Fabian Rudolf

National Cancer Institute (R21CA223901)

  • Roger Brent

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

Copyright

© 2021, Azizoglu 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

  • 2,855
    views
  • 289
    downloads
  • 28
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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. Asli Azizoglu
  2. Roger Brent
  3. Fabian Rudolf
(2021)
A precisely adjustable, variation-suppressed eukaryotic transcriptional controller to enable genetic discovery
eLife 10:e69549.
https://doi.org/10.7554/eLife.69549

Share this article

https://doi.org/10.7554/eLife.69549

Further reading

    1. Chromosomes and Gene Expression
    2. Genetics and Genomics
    Steven Henikoff, David L Levens
    Insight

    A new method for mapping torsion provides insights into the ways that the genome responds to the torsion generated by RNA polymerase II.

    1. Cell Biology
    2. Chromosomes and Gene Expression
    Bhumil Patel, Maryke Grobler ... Needhi Bhalla
    Research Article

    Meiotic crossover recombination is essential for both accurate chromosome segregation and the generation of new haplotypes for natural selection to act upon. This requirement is known as crossover assurance and is one example of crossover control. While the conserved role of the ATPase, PCH-2, during meiotic prophase has been enigmatic, a universal phenotype when pch-2 or its orthologs are mutated is a change in the number and distribution of meiotic crossovers. Here, we show that PCH-2 controls the number and distribution of crossovers by antagonizing their formation. This antagonism produces different effects at different stages of meiotic prophase: early in meiotic prophase, PCH-2 prevents double-strand breaks from becoming crossover-eligible intermediates, limiting crossover formation at sites of initial double-strand break formation and homolog interactions. Later in meiotic prophase, PCH-2 winnows the number of crossover-eligible intermediates, contributing to the designation of crossovers and ultimately, crossover assurance. We also demonstrate that PCH-2 accomplishes this regulation through the meiotic HORMAD, HIM-3. Our data strongly support a model in which PCH-2’s conserved role is to remodel meiotic HORMADs throughout meiotic prophase to destabilize crossover-eligible precursors and coordinate meiotic recombination with synapsis, ensuring the progressive implementation of meiotic recombination and explaining its function in the pachytene checkpoint and crossover control.