1. Chromosomes and Gene Expression
  2. Developmental Biology

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
https://doi.org/10.7554/eLife.61635
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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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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.

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

Share this article

https://doi.org/10.7554/eLife.61635

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Further reading

    1. Chromosomes and Gene Expression
    2. Developmental Biology

    Unified bursting strategies in ectopic and endogenous even-skipped expression patterns

    Augusto Berrocal, Nicholas C Lammers ... Michael B Eisen
    Research Advance

    Transcription often occurs in bursts as gene promoters switch stochastically between active and inactive states. Enhancers can dictate transcriptional activity in animal development through the modulation of burst frequency, duration, or amplitude. Previous studies observed that different enhancers can achieve a wide range of transcriptional outputs through the same strategies of bursting control. For example, in Berrocal et al., 2020, we showed that despite responding to different transcription factors, all even-skipped enhancers increase transcription by upregulating burst frequency and amplitude while burst duration remains largely constant. These shared bursting strategies suggest that a unified molecular mechanism constraints how enhancers modulate transcriptional output. Alternatively, different enhancers could have converged on the same bursting control strategy because of natural selection favoring one of these particular strategies. To distinguish between these two scenarios, we compared transcriptional bursting between endogenous and ectopic gene expression patterns. Because enhancers act under different regulatory inputs in ectopic patterns, dissimilar bursting control strategies between endogenous and ectopic patterns would suggest that enhancers adapted their bursting strategies to their trans-regulatory environment. Here, we generated ectopic even-skipped transcription patterns in fruit fly embryos and discovered that bursting strategies remain consistent in endogenous and ectopic even-skipped expression. These results provide evidence for a unified molecular mechanism shaping even-skipped bursting strategies and serve as a starting point to uncover the realm of strategies employed by other enhancers.

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    Transcription: The plusses and minuses of DNA torsion

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

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    The conserved ATPase PCH-2 controls the number and distribution of crossovers by antagonizing their formation in Caenorhabditis elegans

    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.