Identification of mRNA subsets interacting to RNA binding proteins in regenerating axons
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE103444 | GEO | 2018/12/21
REPOSITORIES: GEO
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Project description:We previously identified that the RNA binding protein Nucleolin is localized to axons of DRG sensory neurons by interaction with the molecular motor Kinesin-1 (Kif5A) and subsequently localizes importin beta1 mRNA there (Perry et al., 2016). To further identify additional RNAs that are localized to axons in a similar mechanism, we immunopercipitated Kif5A from dorsal roots (centrally projecting axons) or Sciatic nerves (peripherally projecting axons), isolated the bound RNA and sequnced it.
2021-07-23 | GSE142099 | GEO
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.
2023-07-25 | GSE230066 | GEO
Project description:Efficient growth cone regeneration requires protein synthesis in the adult mammalian brain and spinal cord. Recent evidence suggests that the local availability of protein synthesis machinery in adult mammalian axons may be an indicator of their regenerative capacity. Here we investigated the local protein synthesis capacity in matured cortical axons, which have poor regenerative capacity, yet are critical for recovery following injury due to traumatic brain injury and stroke. This work is the first to biochemically isolate and identify mRNA from mammalian cortical axons, making use of a unique microfluidic platform to isolate axons free of other cellular debris. We first sought to identify mRNA in naïve axons that makes up the pool of mRNA available for translation initiated following axotomy. Next, we investigated changes in the mRNA population localized to axons 2 days following axotomy and growth cone regeneration. Experiment Overall Design: Cortical axons were harvested using the compartmentalized microfluidic platform after 13 days in culture at a time when they express mature synaptic proteins. A total of 7 Genechips were used for the uninjured cortical axons from 3 different culture batches. 3 Genechips were used for neurons isolated from the neuronal compartment of the microfluidic platfrom. The neuronal Genechip were used to compare mRNA populations with axonal Genechips and for quality control purposes. 3 Genechips were used for regenerating axons; for these, axons were axotomized at 11 days in culture, then allowed to regrow for 2 days before harvesting.
2009-01-14 | E-GEOD-11730 | biostudies-arrayexpress
Project description:Receptor-specific interactome as a hub for rapid cue-induced selective translation in axons
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Project description:Skeletal muscle stem cells, or satellite cells (SCs), are essential to regenerate and maintain muscle. Quiescent SCs reside in an asymmetric niche between the basal lamina and myofiber membrane. To repair muscle, SCs activate, proliferate, and differentiate, fusing to repair myofibers or reacquiring quiescence to replenish the SC niche. Little is known about when SCs reacquire quiescence during regeneration or the cellular processes that direct SC fate decisions and progression through myogenesis. Single cell sequencing of myogenic cells in regenerating muscle identifies SCs reacquiring quiescence and reveals that non-cell autonomous signaling networks influence SC fate decisions during regeneration. Single cell RNA-sequencing of regenerating skeletal muscle reveals that RBP expression, including numerous neuromuscular disease-associated RBPs, is temporally regulated in skeletal muscle stem cells and correlates to stages of myogenic differentiation. By combining machine learning with RBP engagement scoring, we discover that the neuromuscular disease associated RBP Hnrnpa2b1 is a differentiation-specifying regulator of myogenesis controlling myogenic cell fate transitions during terminal differentiation.
2022-06-11 | GSE205690 | GEO
Project description:The subcellular localization of specific mRNAs is an evolutionary conserved mechanism that underlies the establishment of cellular polarity and specialized cell functions. In neurons, mRNA trafficking and local protein translation in dendrites provides an important mechanism that mediates synaptic development and plasticity. The significance of mRNA targeting and protein synthesis in axons, however, is still unclear. Only a small number of transcripts have been identified in axons to date, and their contribution to axon growth and neuronal survival remains largely unknown. Here, we report the results of a novel screen that allowed the separate identification of mRNAs localized in cell bodies and in axons of developing neurons. Using compartmentalized cultures of sympathetic neurons and Sequential Analysis of Gene Expression (SAGE), the screen identified more than 200 axonal mRNAs, including ones that encode cytoskeletal proteins and proteins that function in neural development and signal transduction. Importantly, several classes of transcripts were selectively enriched in axons, indicating that an active process drives the targeting of specific mRNAs from the cell bodies to the axons. This study is the first comprehensive and unbiased analysis of mRNA localization in subcellular domains of any neuronal cell type. We used compartmentalized chambers to culture neonatal rat sympathetic neurons (Campenot, 1977). In these cultures, the cell bodies are separated from the distal axons by a 1 mm wide Teflon divider, which maintains the cell bodies and axon terminals in separate fluid compartments. Primary rat sympathetic neurons are especially suitable for compartmentalized culture because they can be grown as a highly homogeneous population without glial cells. Neurons were seeded in the central compartment with nerve growth factor (NGF), and after a few days, the NGF was lowered in this compartment and supplied only to the peripheral compartment to stimulate axon growth. The anti-mitotic agent cytosine arabinoside C (Ara-C) was added to both compartments to remove non-neuronal cells. mRNA was then isolated after 12 days in culture (DIV) from cell body or axon compartments. As the initial mRNA content in axons was not sufficient to perform the SAGE analysis, both axon and cell body mRNAs were subjected to two rounds of linear amplification to obtain antisense RNA (aRNA). The amplified aRNA was then reverse transcribed and second strand synthesis was performed to proceed with the SAGE assay using the LongSAGE kit (Invitrogen) according to the manufacturer’s protocol.
2010-01-30 | E-GEOD-13788 | biostudies-arrayexpress
Project description:Local mRNA translation mediates the adaptive responses of axons to extrinsic signals but direct evidence that it occurs in mammalian CNS axons in vivo is scant. We developed an axon-TRAP-RiboTag approach in mouse that allows deep-sequencing analysis of ribosome-bound mRNAs in the retinal ganglion cell axons of the developing and adult retinotectal projection in vivo. The embryonic-to-postnatal axonal translatome comprises an evolving subset of enriched genes with axon-specific roles suggesting distinct steps in axon wiring, such as elongation, pruning and synaptogenesis. Adult axons, remarkably, have a complex translatome with strong links to axon survival, neurotransmission and neurodegenerative disease. Translationally co-regulated mRNA subsets share common upstream regulators, and novel sequence elements generated by alternative splicing that promote axonal mRNA translation. Our results indicate that intricate regulation of compartment-specific mRNA translation in mammalian CNS axons supports the formation and maintenance of neural circuits in vivo. The profiling of ribosome-bound mRNAs in mouse retinal ganglion cell axons at 4 different developmental stages
2016-06-16 | E-GEOD-79352 | biostudies-arrayexpress
Project description:We report that delta cells are Sox9 descendants that expand at the periphery of the regenerating islets following partial pancreatectomy. We further characterize regeneration-driven heterogeneity of beta cells at a single-cell resolution, demonstrating sub-populations of ER-stressed, proliferating and highly-functioning beta-cells. We further systematically map sub populations of beta-cells that are paired with other endocrine cell types. Our analysis suggests that the particular cluster of beta-cells that pair with delta-cells benefits from stress protection, implying that the interaction between beta and delta-cells safeguards against regeneration-associated challenges.
2021-09-10 | GSE183788 | GEO
Project description:Regenerating intestine tissues were compared with normal (non-regenerating tissues) to determine the gene expression profile at early stages of regeneration (3, 7 and 14 days post- evisceration (dpe)). Immuno activated tissues with LPS were compared with Normal (non-regenerating tissues) and regenerating tissues (3 and 7 dpe) to determine the gene expression of immune related genes in the sea cucumber and it's expression during early stages of regeneration. 16 Total arrays. 8 comparisons with 8 dye swap replicates. Normal Vs. (3, 7 and 14 days of regeneration), and Vs. (LPS) 2 microarray slides used. Each slide with 8 Arrays (8 x 15k). 15,744 probes printed per array. (all 16 arrays are identically printed). 7,209 ESTs from Normal, 3 dpe and 7 dpe tissues were used to design the probes. Two probes per EST from diferent regions of the sequence (as a technical replicate). 536 technical controls and more than 600 internal biological controls (from different species).
2010-05-18 | E-GEOD-16182 | biostudies-arrayexpress
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