Evidence map›Paper›PMID 38260569›Full record

ArticlebioRxiv : the preprint server for biology2025

Single-cell transcriptional dynamics in a living vertebrate.

Elizabeth Eck, Bruno Moretti, Brandon H Schlomann, Jordão Bragantini, Merlin Lange, Xiang Zhao, Shruthi VijayKumar, Guillaume Valentin, Cristina Loureiro, Pablo Perez Franco and 5 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed, 16 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

15 authors at 6 institutions in 4 countries.

Elizabeth EckBiophysics Graduate Group, University of California, Berkeley, CA, USA.
Bruno MorettiDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.ORCID 0000-0003-1665-1548
Brandon H SchlomannDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.ORCID 0000-0003-2280-0132
Jordão BragantiniChan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
Merlin LangeChan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
Xiang ZhaoChan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
Shruthi VijayKumarChan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
Guillaume ValentinCenter of PhenoGenomics, School of Life Sciences, EPFL; Swiss Federal Institute of Technology Lausanne, CH.
Cristina LoureiroInstitute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology Lausanne EPFL, CH.
Pablo Perez FrancoInstitute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology Lausanne EPFL, CH.
Chloé JollivetInstitute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology Lausanne EPFL, CH.
Baldemar MotomochiDepartment of Molecular and Cell Biology, University of California, Merced, CA, USA.ORCID 0009-0006-8071-0644
Loïc A RoyerChan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.ORCID 0000-0002-9991-9724
Andrew C OatesInstitute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology Lausanne EPFL, CH.ORCID 0000-0002-3015-3978
Hernan G GarciaDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.ORCID 0000-0002-5212-3649
Chan Zuckerberg Initiative (United States) · USÉcole Polytechnique Fédérale de Lausanne · CHQB3 · USUniversity of California, Berkeley · USThe Francis Crick Institute · GBUniversity of California, Merced · US

Funding

Uncovering single-cell transcriptional dynamics in somitogenesis in live zebrafish embryosR21HD107436 · NICHD · UNIVERSITY OF CALIFORNIA BERKELEY · PI GARCIA, HERNAN GUSTAVO · 2023 to 2023
$441k
NICHD NIH HHS R21 HD107436Wellcome Trust
6 · The paper itself

Abstract

The ability to quantify transcriptional dynamics in individual cells via live imaging has revolutionized our understanding of gene regulation. However, such measurements are lacking in the context of vertebrate embryos. We addressed this deficit by applying MS2-MCP mRNA labeling to the quantification of transcription in zebrafish, a model vertebrate. We developed a platform of transgenic organisms, light sheet fluorescence microscopy, and optimized image analysis that enables visualization and quantification of MS2 reporters. With these tools, we obtained single-cell, real-time measurements of transcriptional dynamics of the segmentation clock. Our measurements challenge the traditional view of smooth clock oscillations and instead suggest a model of discrete transcriptional bursts that are organized in space and time. Together, these results highlight how measuring single-cell transcriptional activity in the context of vertebrate organisms can reveal unexpected features of gene regulation and how this data can fuel the dialogue between theory and experiment.

Identifiers

PMID38260569
PMCPMC10802376
OpenAlexW4390649768

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.