Identifying Transcription Factors Expressed by V0v Spinal Cord Interneurons
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE83723 | GEO | 2016/08/26
SECONDARY ACCESSION(S): PRJNA326872
REPOSITORIES: GEO
Similar Datasets
Project description:The goals of this study is to compare transcriptome profiles (RNA-seq) of zebrafish V2a interneurons with regrown axon and those without regrown axon in the spinal segments rostral to the lesion after spinal cord injury. For purification of V2a interneurons with regrown axon, the fluorescent tracer Rhodamine Dextran (RD) was retrogradely applied to Tg(Chx10:GFP) fish at three or eight weeks post injury. Spinal cord segments rostral to the lesion site was collected from 20 fish at 3- or 8 wpi, and corresponding spinal cord segments from 20 uninjured fish were collected as control material. GFP+/RD+ and GFP+/RD- cells were FAC-sorted and subjected to RNA-sequencing. Total RNA was isolated using SMART-SeqTM v4 UltraTM Low Input RNA Kit for Sequencing (Clontech). Sequencing libraries (N=5-6) were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina following the manufacturer’s instructions (NEB). We mapped about 40-80 million sequence reads per sample to the zebrafish genome and identified 42,370 transcripts in the zebrafish V2a interneurons in the spinal cord. Our study represents the detailed analysis of transcriptomes of zebrafish V2a interneurons with regrown axon and those without regrown axon in the spinal segments rostral to the lesion after spinal cord injury.
2022-09-13 | GSE213081 | GEO
Project description:In this report, we describe a successful protocol for isolating and expression-profiling live fluorescent- protein-labelled neurons from zebrafish embryos. As a proof-of-principle for this method, we FAC-sorted and RNA-profiled GFP-labelled spinal CiA interneurons and compared the expression profile of these cells to those of post-mitotic spinal neurons in general and to all trunk cells. We show that RNA of sufficient quality and quantity to uncover both expected and novel transcription profiles via Affymetrix microarray analysis can be extracted from 5,700 to 20,000 FAC-sorted cells. As part of this study, we also further confirm the genetic homology of mammalian and zebrafish V1 interneurons, by demonstrating that zebrafish V1 cells (CiAs) express genes that encode for the transcription factors Lhx1a and Lhx5. This protocol for dissociating, sorting and RNA-profiling neurons from organogenesis-stage zebrafish embryos should also be applicable to other developing organs and tissues and potentially other model organisms.
2020-02-26 | GSE145916 | GEO
Project description:Spinal inhibitory interneurons play crucial roles in shaping motor output, but the molecular heterogeneity contained within cardinal spinal interneuron populations is unclear. This experiment was designed to identify genes enriched in the Engrailed1 (En1) population of ventral V1 inhibitory interneurons relative to the Ptf1a population of dorsal dI4/dILA interneurons, with the goal of identifying genetic markers for discrete V1 subpopulations.
2016-01-15 | GSE69560 | GEO
Project description:Here we compare the gene expression profiles of two distict, fluorescently identified neuronal populations, the motor neruons (MN) and the decending commissural interneurons (dCIN) of the neonatal rat spinal cord isolated with laser microdissection. These two populations participate in the neuronal networks in the spinal cord where they have destinct functions in shaping (dCINs) and transferring the output to the muscles (MNs) during locomotion. We wished to determine how the functinal differences in these nerurons are manifested at the gene expression level. Experiment Overall Design: Neurons were retrogradely labelled with rhodamine through application of the tracer to cut axons followed by incubation in oxygenated Ringer solution. Spinal cord were then snap frozen, cryosectioned and fluorescent single cells were laser dissected into a collector tube to a total of ca. 50-200 cells pr sample. RNA was then extracted, two round amplified and hybridized to Affymatrix RNU-34 chips. 22 samples were hybridized onto chips, 7 MNs, 7 CINS and 8 MIX.
2008-06-16 | E-GEOD-9439 | biostudies-arrayexpress
Project description:Background: V0v spinal interneurons are highly-conserved, glutamatergic, commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However, we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks, we FAC-sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression-profiled them using microarrays and scRNA-seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild-type siblings. Results: Our data reveal two molecularly-distinct subtypes of V0v spinal interneurons at 48 h and suggest that, by this stage of development, evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons, or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons, plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly, we show that Hmx2/3a, repress dI2 interneuronal expression of skor1a and nefma, two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly-distinct subsets of V0v spinal interneurons, as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2, V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then, later, start to express markers of distinct types of inhibitory spinal interneurons, or motoneurons. Taken together, our findings significantly increase our knowledge of V0v spinal development and move us closer towards the essential goal of identifying the complete gene regulatory networks that specify this crucial cell type.
2023-08-09 | GSE240239 | GEO
Project description:Background: V0v spinal interneurons are highly-conserved, glutamatergic, commissural neurons that function in locomotor circuits. We have previously shown that Evx1 and Evx2 are required to specify the neurotransmitter phenotype of these cells. However, we still know very little about the gene regulatory networks that act downstream of these transcription factors in V0v cells. Methods: To identify candidate members of V0v gene regulatory networks, we FAC-sorted WT and evx1;evx2 double mutant zebrafish V0v spinal interneurons and expression-profiled them using microarrays and scRNA-seq. We also used in situ hybridization to compare expression of a subset of candidate genes in evx1;evx2 mutants and wild-type siblings. Results: Our data reveal two molecularly-distinct subtypes of V0v spinal interneurons at 48 h and suggest that, by this stage of development, evx1;evx2 double mutant cells transfate into either inhibitory spinal interneurons, or motoneurons. Our results also identify 25 transcriptional regulator genes that require Evx1/2 for their expression in V0v interneurons, plus a further 11 transcriptional regulator genes that are repressed in V0v interneurons by Evx1/2. Two of the latter genes are hmx2 and hmx3a. Intriguingly, we show that Hmx2/3a, repress dI2 interneuronal expression of skor1a and nefma, two genes that require Evx1/2 for their expression in V0v interneurons. This suggests that Evx1/2 might regulate skor1a and nefma expression in V0v interneurons by repressing Hmx2/3a expression. Conclusions: This study identifies two molecularly-distinct subsets of V0v spinal interneurons, as well as multiple transcriptional regulators that are strong candidates for acting downstream of Evx1/2 to specify the essential functional characteristics of V0v interneurons. Our data further suggest that in the absence of both Evx1 and Evx2, V0v spinal interneurons initially change their neurotransmitter phenotypes from excitatory to inhibitory and then, later, start to express markers of distinct types of inhibitory spinal interneurons, or motoneurons. Taken together, our findings significantly increase our knowledge of V0v spinal development and move us closer towards the essential goal of identifying the complete gene regulatory networks that specify this crucial cell type.
2023-08-09 | GSE240238 | GEO
Project description:We present a transcriptomic atlas of spinal V1 interneurons across postnatal development (P0, P14, P28, and P56) in the mouse using single-nucleus RNA sequencing (snRNA-seq). We also present transcriptomic data comparing V1 interneurons in En1 heterozygous and En1 KO mice at age P0 only.
2024-09-02 | GSE275595 | GEO
Project description:Promoting residential cells, particularly endogenous neural stem and progenitor cells (NSPCs), for tissue regeneration represents a potential strategy for the treatment of spinal cord injury (SCI). However, adult NSPCs differentiate mainly into glial cells and contribute to glial scar formation at the site of injury. Gsx1 is known to regulate the generation of excitatory and inhibitory interneurons during embryonic development of the spinal cord. Here we show that lentivirus-mediated expression of Gsx1 increases the number of NSPCs in a mouse model of lateral hemisection SCI during the acute stage. Subsequently, Gsx1 expression increases the generation of glutamatergic and cholinergic interneurons and decreases the generation of GABAergic interneurons in the chronic stage of SCI. Importantly, Gsx1 reduces reactive astrogliosis and glial scar formation, promotes 5-HT neuronal activity, and improves the locomotor function of the injured mice. Moreover, RNA-seq analysis reveals that Gsx1-induced transcriptome regulation correlates with NSPC signaling, NSPC activation, neuronal differentiation, and inhibition of astrogliosis and scar formation. Collectively, our study provides molecular insights for Gsx1-mediated functional recovery and identifies Gsx1 gene regulation as a potential application for injuries in the spinal cord and possibly other parts of the central nervous system.
2021-05-01 | GSE171441 | GEO
Project description:Next Generation Sequencing of zebrafish V2a interneurons in spinal segments rostral to the lesion after spinal cord injury
| PRJNA879067 | ENA
Project description:Neuronal diversification is a fundamental step in the construction of functional neural circuits, yet how neurons generated from single progenitor domains acquire diverse subtype identities remains poorly understood. Here, we developed a stem cell-based system to model subtype diversification of V1 interneurons, a class of spinal neurons comprising four clades, each containing dozens of molecularly distinct neuronal subtypes. We demonstrate that V1 subtype diversity is not hard-wired and can be modified by extrinsic signals. Inhibition of Notch and activation of retinoid signaling results in a switch to MafA clade identity and enriches differentiation of Renshaw cells, a specialized MafA subtype that mediates recurrent inhibition of spinal motor neurons. We show that in vitro-generated Renshaw cells migrate into appropriate spinal laminae upon transplantation and form subtype-specific synapses with motor neurons. Our results demonstrate that stem cell-derived neuronal subtypes can be used to investigate mechanisms underlying neuronal subtype specification and circuit assembly.
2018-10-07 | GSE112377 | GEO