Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene

  1. Augusto Berrocal
  2. Nicholas C Lammers
  3. Hernan G Garcia  Is a corresponding author
  4. Michael B Eisen  Is a corresponding author
  1. University of California, Berkeley, United States

Abstract

We used live imaging to visualize the transcriptional dynamics of the Drosophila melanogaster even-skipped gene at single-cell and high temporal resolution as its seven stripe expression pattern forms, and developed tools to characterize and visualize how transcriptional bursting varies over time and space. We find that despite being created by the independent activity of five enhancers, even-skipped stripes are sculpted by the same kinetic phenomena: a coupled increase of burst frequency and amplitude. By tracking the position and activity of individual nuclei, we show that stripe movement is driven by the exchange of bursting nuclei from the posterior to anterior stripe flanks. Our work provides a conceptual, theoretical and computational framework for dissecting pattern formation in space and time, and reveals how the coordinated transcriptional activity of individual nuclei shape complex developmental patterns.

Data availability

All of the raw and processed data described in this paper are available on Data Dryad at doi:10.6078/D1XX33 and computational notebooks with necessary data to regenerate analyses and figures is available in File S1 and at https://github.com/mbeisen/Berrocal_2020.

The following data sets were generated

Article and author information

Author details

  1. Augusto Berrocal

    Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6506-9071
  2. Nicholas C Lammers

    Biophysics Graduate Group, University of California, Berkeley, Oakland, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6832-6152
  3. Hernan G Garcia

    Molecular and Cell Biology, Physics, University of California, Berkeley, Berkeley, United States
    For correspondence
    hggarcia@berkeley.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5212-3649
  4. Michael B Eisen

    Department of Molecular and Cell Biology and HHMI, University of California, Berkeley, Berkeley, United States
    For correspondence
    mbeisen@gmail.com
    Competing interests
    Michael B Eisen, Editor-in-Chief, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7528-738X

Funding

Howard Hughes Medical Institute (Investigator Award)

  • Michael B Eisen

National Science Foundation (1652236)

  • Hernan G Garcia

National Institutes of Health (DP2-OD024541-01)

  • Hernan G Garcia

National Institutes of Health (5T32HG000047-18)

  • Nicholas C Lammers

University of California Institute for Mexico and the United States (NA)

  • Augusto Berrocal

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

Reviewing Editor

  1. Robert H Singer, Albert Einstein College of Medicine, United States

Publication history

  1. Received: July 31, 2020
  2. Accepted: October 9, 2020
  3. Accepted Manuscript published: December 10, 2020 (version 1)
  4. Version of Record published: February 5, 2021 (version 2)

Copyright

© 2020, Berrocal 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. Augusto Berrocal
  2. Nicholas C Lammers
  3. Hernan G Garcia
  4. Michael B Eisen
(2020)
Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene
eLife 9:e61635.
https://doi.org/10.7554/eLife.61635

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