Spinal Cord Injury regulates circular mRNA expression in axons
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA957300 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24216549_1.fastq.gz | Fastqsanger.gz | |||
| SRR24216549_2.fastq.gz | Fastqsanger.gz | |||
| SRR24216550_1.fastq.gz | Fastqsanger.gz | |||
| SRR24216550_2.fastq.gz | Fastqsanger.gz | |||
| SRR24216551_1.fastq.gz | Fastqsanger.gz |
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Project description:Injured axons in the CNS do not spontaneously regenerate leading to paralysis. Neurons can transport RNA and ribosomes to the site of injury where de novo translation has been known to occur, facilitating repair. Yet the tools available for studying axonal specific RNA are limited. We came up with a simple modification using Cold Active Proteases that enabled us to enrich for axonal RNA from rats with spinal cord injury (SCI) compared to non-injured. Our enriched axonal prep was then analyzed by bulk RNA-seq, where we looked at total RNA and we found differentially expressed genes (DEGs). Analyzing our bulk RNA-seq by Gene Ontology, we found the second most significant pathway for all DEGs was for axonogenesis, with markedly low glial cell contamination. From our DEGs we detected Rims2, which is reported to be predominately a circular RNA (circRNA) in the rodent CNS. Upon further annotation, we found over 200 putative circRNAs. circRNAs are abundant and well conserved in the brain, they are thought to be transcriptional regulators by functioning as microRNA (miR) sponges or binding to RNA-binding proteins (RBPs). By computational analysis using Circular RNA Interactome, we are able to predict which miRs or RBPs could bind to circRims2.
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Project description:Adult zebrafish have the ability to recover from spinal cord injury and exhibit re-growth of descending axons from the brainstem to the spinal cord. We performed gene expression analysis using microarray to find damage-induced genes after spinal cord injury, which shows that Sox11b mRNA is up-regulated at 11 days after injury. However, the functional relevance of Sox11b for regeneration is not known. Here, we report that the up-regulation of Sox11b mRNA after spinal cord injury is mainly localized in ependymal cells lining the central canal and in newly differentiating neuronal precursors or immature neurons. Using an in vivo morpholino-based gene knockout approach, we demonstrate that Sox11b is essential for locomotor recovery after spinal cord injury. In the injured spinal cord, expression of the neural stem cell associated gene, Nestin, and the proneural gene Ascl1a (Mash1a), which are involved in the self-renewal and cell fate specification of endogenous neural stem cells, respectively, is regulated by Sox11b. Our data indicate that Sox11b promotes neuronal determination of endogenous stem cells and regenerative neurogenesis after spinal cord injury in the adult zebrafish. Enhancing Sox11b expression to promote proliferation and neurogenic determination of endogenous neural stem cells after injury may be a promising strategy in restorative therapy after spinal cord injury in mammals. Spinal cord injury or control sham injury was performed on adult zebrafish. After 4, 12, or 264 hrs, a 5 mm segment of spinal cord was dissected and processed (as a pool from 5 animals) in three replicate groups for each time point and treatment.
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Project description:To determine whether the expression levels of circular RNAs were altered and lay a foundation for future work, we used high-throughput microarray analysis to screen circular RNAs expression patterns in the spinal cord of adult rats after traumatic spinal cord injury (SCI), finally to evaluate the potential rat models as a platform for the development of novel therapeutic targets for spinal cord injury in future clinical studies. Overall six rats at 3 days post-SCI in two groups were used to perform the microarray.
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Project description:Adult zebrafish have the ability to recover from spinal cord injury and exhibit re-growth of descending axons from the brainstem to the spinal cord. We performed gene expression analysis using microarray to find damage-induced genes after spinal cord injury, which shows that Sox11b mRNA is up-regulated at 11 days after injury. However, the functional relevance of Sox11b for regeneration is not known. Here, we report that the up-regulation of Sox11b mRNA after spinal cord injury is mainly localized in ependymal cells lining the central canal and in newly differentiating neuronal precursors or immature neurons. Using an in vivo morpholino-based gene knockout approach, we demonstrate that Sox11b is essential for locomotor recovery after spinal cord injury. In the injured spinal cord, expression of the neural stem cell associated gene, Nestin, and the proneural gene Ascl1a (Mash1a), which are involved in the self-renewal and cell fate specification of endogenous neural stem cells, respectively, is regulated by Sox11b. Our data indicate that Sox11b promotes neuronal determination of endogenous stem cells and regenerative neurogenesis after spinal cord injury in the adult zebrafish. Enhancing Sox11b expression to promote proliferation and neurogenic determination of endogenous neural stem cells after injury may be a promising strategy in restorative therapy after spinal cord injury in mammals.
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