Analysis of RNA localization in nucleolin deficient axons
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA595902 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We previously showed 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). In this work, we created a mouse with a heterozygous deletion of the domain in nucleolin responsible for the Kif5A interaction and showed that nucelolin protein levels are reduced in the axons of dorsal root ganglia neurons in this mouse model. The goal of this study was to identify RNAs who's axonal localization is affected by this perturbation.
2021-07-23 | GSE142096 | GEO
Project description:We previously showed that importin beta1 local translation in injured axons is a key event in injury-signaling and regeneration (Perry et al., 2012). Next, we showed that importin beta1 is localize to axons through a localization motif in its 3'UTR and that this motif is bound by the RNA binding proteins Nucleolin and PTBP1. In this study, we asked which other RNA targets are bound by these two RNA binding proteins in naive Sciatic nerves and how are they changing 7 days after injury.
2021-07-23 | GSE142107 | GEO
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:GAR-Driven Subcellular Localization of the Growth Controlling RNA Binding Protein Nucleolin
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Project description:To further explore the function and underlying mechanism of nucleolin in embryonic stem cells (ESCs), we compared the transcription profile of tetracycline (Tc)-inducible EGFP (as a control) or nucleolin siRNA expression-stable ESCs cultured with or without Tc for 3 days, and identified distinct classes of up- and down-regulated genes by nucleolin in mouse ESCs. Total RNA obtained from CGR8 ES cells stably integrated with Tc-inducible siRNA EGFP, nucleoin-1 or nucleolin-2 cultured with or without Tc for 3 days, and then hybridized to Illumina Sentrix Mouse-6 v2.0 BeadChips. Three replicates each condition.
2011-10-19 | E-GEOD-23993 | biostudies-arrayexpress
Project description:Although Rrp6 contains a helicase and RNase D domain at the C-terminus, it is not involved in stable RNA interactions. We thus hypothesized that mRrp6-mediated nucleolar inflammatory RNA degradation may depend on the pre-mRNA substrate that is delivered to the mRrp6-exosome complex by nucleolin as a guide factor. To demonstrate this possibility, we examined nucleoplasmic RNAs which were bound to nucleolin through RNA-IP-sequencing at the late time points of LPS stimulation.
2021-02-28 | GSE95528 | GEO
Project description:To further explore the function and underlying mechanism of nucleolin in embryonic stem cells (ESCs), we compared the transcription profile of tetracycline (Tc)-inducible EGFP (as a control) or nucleolin siRNA expression-stable ESCs cultured with or without Tc for 3 days, and identified distinct classes of up- and down-regulated genes by nucleolin in mouse ESCs.
2011-10-20 | GSE23993 | GEO
Project description:Covalently closed circular DNA (cccDNA) forms the basis for replication and persistence of hepatitis B virus (HBV) in the chronically infected liver. In this study we sought to identify host factors interacting with the HBV genome. Nucleolin (Ncl) was identified as a potential interactor of HBV cccDNA. This interaction was veriefied using an established ChIPseq protocol. The data show that Ncl binds cccDNA albeit at lower levels than HBcAg. Ncl deposition occurs across the genome without a clear localization and a variable pattern of deposition between experiments. This verifies the interaction of Ncl with HBV-cccDNA.
2021-12-31 | GSE123715 | 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: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.
2010-01-31 | GSE13788 | GEO