ScMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities
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ABSTRACT:
PROVIDER: PRJNA926672 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23195960_1.fastq.gz | Fastqsanger.gz | |||
| SRR23195960_2.fastq.gz | Fastqsanger.gz | |||
| SRR23195961_1.fastq.gz | Fastqsanger.gz | |||
| SRR23195961_2.fastq.gz | Fastqsanger.gz | |||
| SRR23195962_1.fastq.gz | Fastqsanger.gz |
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Project description: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 mature hindbrain consists of alternating odd- versus even-type rhombomeres, our scMultiome analyses do not detect extensive odd versus even 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 mature rhombomeres requires resolution of these mixed-identity cell states.
2023-08-08 | GSE223535 | GEO
Project description: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 mature hindbrain consists of alternating odd- versus even-type rhombomeres, our scMultiome analyses do not detect extensive odd versus even 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 mature rhombomeres requires resolution of mixed transcription and chromatin states.
| S-EPMC9900950 | biostudies-literature
Project description: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 has 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 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 the resolution of mixed transcription and chromatin states.
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Project description:Hoxb1 is required for proper specification of rhombomere 4 and the facial motor neurons. This study analyzed gene expression in the corresponding hindbrain segment of E10.5 mutant embryos. Several genetic pathways were found altered, including transcription factors such as Phox2b, Gata3, Nkx2-2 and Nkx6-1. Keywords: hindbrain development, rhombomere 4, Hoxb1
2006-08-28 | GSE5126 | GEO
Project description:This study analyzed mRNA profiles in rhombomere 4 of E10.5 mouse knock-in embryos expressing either normal endogenous Hox-B1 protein or the paralogous Hox-A1 protein from the Hoxb1 locus. The Hox-A1 protein was found to be detectably less efficacious than Hox-B1 in promoting neurogenesis in the basal plate of rhombomere 4 and its transcriptional profile shared several similarities with the Hoxb1 mutant. Keywords: gene swap, knock-in, hindbrain development, rhombomere 4
2006-08-28 | GSE5124 | GEO
Project description:Hoxb1 is required for proper specification of rhombomere 4 and the facial motor neurons. This study analyzed gene expression in the corresponding hindbrain segment of E10.5 mutant embryos. Several genetic pathways were found altered, including transcription factors such as Phox2b, Gata3, Nkx2-2 and Nkx6-1. Experiment Overall Design: Each of the three mutant and control samples was an independent biological replicate. Pools of r4 segments from multiple embryos were snap frozen on dry ice and stored at -80ºC. Total RNA was isolated, processed with standard Affymetrix protocols and hybridized to GeneChip Mouse Expression Sets 430A.
2008-06-13 | E-GEOD-5126 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to understand the progressive patterning of neurogenesis of the developing zebrafish hindbrain. 16hpf, 24hpf and 44hpf zebrafish hindbrains were used for single-cell RNA-sequencing with the aim to uncover hindbrain development. Methods: 40 microdissected hindbrains per each stage were dissociated at loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina HiSeq 4000. Conclusions: Our study constitute a resource of hindbrain gene expression during development. We have identified transcriptional programs involved in: rhombomere segmental identity, dorso-ventral patterning, boundary and centre progenitor cells and temporal regulation of neurogenesis.
2019-12-05 | GSE141427 | GEO
Project description:During development, rhombomere 1 gives rise to a multitude of cell types, including serotonergic as well as glutamatergic neurons that populate the raphe nuclei. Transcription factor Gata2 has been shown to regulate the development of the serotonergic neurons in the rhombomere 1. To further understand the role and targets of Gata2 in the rhombomere 1 during development, we used cDNA microarrays to compare gene expression in the embryonic day 12.5 (E12.5) rhombomere 1 tissues extracted from wild-type and Gata2 mutant embryos.
2016-11-01 | GSE89354 | GEO
Project description:Serotonin (5-HT) neurons, the major components of the raphe nuclei, arise from ventral hindbrain progenitors. Based on the anatomical location and axonal projection, 5-HT neurons are coarsely divided into rostral and caudal groups. Here, we propose a novel strategy to generate hindbrain 5-HT neurons from human pluripotent stem cells (hPSCs), which involves the formation of ventral-type neural progenitor cells (NPCs) and stimulation of the hindbrain 5-HT neural development. A caudalizing agent, retinoid acid (RA), was used to direct the cells into the hindbrain cell fate. Approximately 30-40% of hPSCs successfully developed into 5-HT-expressing neurons using our protocol, with the majority acquiring a caudal rhombomere identity (r5-8). We further modified our monolayer differentiation system to generate 5-HT neuron-enriched hindbrain-like organoids. We have also suggested downstream applications of our 5-HT monolayer and organoid cultures to study neuronal response to gut microbiota. Our methodology could become a powerful tool for future studies related to 5-HT neurotransmission.
2021-04-01 | GSE167278 | GEO
Project description:DNase-seq on postnatal mixed mouse hindbrain For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
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