scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities

Abstract
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Abstract

Rhombomeres serve to position neural progenitors in the embryonic hindbrain, thereby ensuring appropriate neural circuit formation, but the molecular identities of individual rhombomeres and the mechanism whereby they form have not been fully established. Here we apply scMultiome analysis in zebrafish to molecularly resolve all rhombomeres for the first time. We find that rhombomeres become molecularly distinct between 10hpf (end of gastrulation) and 13hpf (early segmentation). While the embryonic hindbrain transiently contains alternating odd- versus even-type rhombomeres, our scMultiome analyses do not detect extensive odd versus even molecular characteristics in the early hindbrain. Instead, we find that each rhombomere displays a unique gene expression and chromatin profile. Prior to the appearance of distinct rhombomeres, we detect three hindbrain progenitor clusters (PHPDs) that correlate with the earliest visually observed segments in the hindbrain primordium and that represent prospective rhombomere r2/r3 (possibly including r1), r4 and r5/r6, respectively. We further find that the PHPDs form in response to Fgf and RA morphogens and that individual PHPD cells co-express markers of multiple mature rhombomeres. We propose that the PHPDs contain mixed-identity progenitors and that their subdivision into individual rhombomeres requires resolution of mixed transcription and chromatin states.

Data availability

scMultiome data has been deposited at GEO under record number GSE223535

The following data sets were generated

(2023) scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities
NCBI Gene Expression Omnibus, GSE223535.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE223535

Article and author information

Author details

Yong-Il Kim

Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, United States

Competing interests
The authors declare that no competing interests exist.
Rebecca O'Rourke

Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-1198-6963
Charles G Sagerström

Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, United States

For correspondence
charles.sagerstrom@cuanschutz.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-1509-5810

Funding

National Institute of Neurological Disorders and Stroke (NS038183)

Charles G Sagerström

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

Ethics

Animal experimentation: The Institutional Animal Care and Use Committee (IACUC) of the University of Colorado Medical School approved all procedures involving zebrafish under protocol #870.

Copyright

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.