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Cited by 207Genomics and Chromatin DynamicsGene Regulatory Network AnalysisDiffusion and Search Dynamics

Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos

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Mir, Mustafa, Stadler, Michael R, Ortiz, Stephan A, Hannon, Colleen E, Harrison, Melissa M, Darzacq, Xavier, Eisen, Michael B·2018·eLife
DOI 10.7554/elife.40497PMC PMC6307861

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Abstract

The regulation of transcription requires the coordination of numerous activities on DNA, yet how transcription factors mediate these activities remains poorly understood. Here, we use lattice light-sheet microscopy to integrate single-molecule and high-speed 4D imaging in developing Drosophila embryos to study the nuclear organization and interactions of the key transcription factors Zelda and Bicoid. In contrast to previous studies suggesting stable, cooperative binding, we show that both factors interact with DNA with surprisingly high off-rates. We find that both factors form dynamic subnuclear hubs, and that Bicoid binding is enriched within Zelda hubs. Remarkably, these hubs are both short lived and interact only transiently with sites of active Bicoid-dependent transcription. Based on our observations, we hypothesize that, beyond simply forming bridges between DNA and the transcription machinery, transcription factors can organize other proteins into hubs that transiently drive multiple activities at their gene targets. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).

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  • Zelda promotes the formation of local transcription factor hubs involving transcription factors required for developmental patterning, such as Bicoid and Dorsal.

    “For instance, Zelda promotes the formation of local TF hubs involving important transcription factors required for developmental patterning, such as Bicoid and Dorsal [51–54].”

    From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [52]

    The Results section ('Bicoid binding events are enriched in Zelda hubs'; page unavailable) reports Bicoid binding enriched within Zelda hubs, supporting that example. The cited paper does not establish Dorsal’s involvement in those hubs, so the Dorsal example is unsupported by this source. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

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Authors
Mir, M., Stadler, M. R., Ortiz, S. A., Hannon, C. E., Harrison, M. M., Darzacq, X., & Eisen, M. B.
Affiliations
  • University of California, Berkeley (US)
  • Howard Hughes Medical Institute (US)
  • University of Wisconsin–Madison (US)
Corresponding author
  • Darzacq, Xavier
  • Eisen, Michael B
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2018-12-27
Volume
7
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.40497
PMC
PMC6307861
OpenAlex
W2949107687
Cited by
207
References
5
Citations by year
2026: 17 · 2025: 24 · 2024: 37 · 2023: 37 · 2022: 21 · 2021: 28 · 2020: 23 · 2019: 16 · 2018: 4
FWCI
6.31
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by)
Funders
  • American Cancer Society
  • National Institutes of Health (GM111694, UO1-EB021236, U54-DK107980)
  • California Institute for Regenerative Medicine (LA1-08013)
  • Howard Hughes Medical Institute
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
Keywords
transcription factor-DNA binding, Zelda, Bicoid, transient protein interactions, transcriptional regulation, Drosophila embryo, nuclear organization, lattice light-sheet microscopy, 4D imaging, single-molecule imaging, dissociation rate constant
MeSH terms
Animals, Binding Sites, Cell Nucleus, Drosophila melanogaster, Embryo, Nonmammalian, Nuclear Proteins, Protein Binding, Transcription Factors, Trans-Activators, Homeodomain Proteins, Gene Expression Regulation, Developmental, Microscopy, Confocal, Imaging, Three-Dimensional, Drosophila Proteins, Time-Lapse Imaging

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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