Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE115480 | GEO | 2019/01/07
REPOSITORIES: GEO
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Project description:To assess neuronal expression divergence between mice and rats, we used the Affymetrix array platform to assay the transcriptomes of micro-dissected individual soma and pool of dendrites of hippocampal neurons in dispersed primary cell cultures from rat and mouse. Using microdissected soma and dendrites from primary cultures of hippocampal neurons of two mouse strains (C57BL/6 and Balb/c) and one rat strain (Sprague-Dawley), we investigate via microarrays, subcellular localization of mRNAs in neurons
2014-10-14 | E-GEOD-61084 | biostudies-arrayexpress
Project description:To assess neuronal expression divergence between mice and rats, we used the Affymetrix array platform to assay the transcriptomes of micro-dissected individual soma and pool of dendrites of hippocampal neurons in dispersed primary cell cultures from rat and mouse. Using microdissected soma and dendrites from primary cultures of hippocampal neurons of two mouse strains (C57BL/6 and Balb/c) and one rat strain (Sprague-Dawley), we investigate via microarrays, subcellular localization of mRNAs in neurons
2014-10-14 | E-GEOD-61085 | biostudies-arrayexpress
Project description:The subcellular localization and translation of messenger RNA (mRNA) supports functional differentiation between cellular compartments. In neuronal dendrites, local translation of mRNA provides a rapid and specific mechanism for synaptic plasticity and memory formation, and might be involved in the pathophysiology of certain brain disorders. Despite the importance of dendritic mRNA translation, little is known about which mRNAs can be translated in dendrites in vivo and when their translation occurs. Here we collect ribosome-bound mRNA from the dendrites of CA1 pyramidal neurons in the adult mouse hippocampus. We find that dendritic mRNA rapidly associates with ribosomes following a novel experience consisting of a contextual fear conditioning trial. High throughput RNA sequencing followed by machine learning classification reveals an unexpected breadth of ribosome-bound dendritic mRNAs, including mRNAs expected to be entirely somatic. Our findings are in agreement with a mechanism of synaptic plasticity that engages the acute local translation of functionally diverse dendritic mRNAs. RNA-Seq of ribosome-bound mRNA immunoprecipitated from dendrites and soma of CA1 pyramidal neurons in the mouse hippocampus
2014-07-30 | E-GEOD-58343 | biostudies-arrayexpress
Project description:Using microdissected dendrites from primary cultures of hippocampal neurons of two mouse strains (C57BL/6 and Balb/c) and one rat strain (Sprague-Dawley), we investigate via microarrays, subcellular localization of mRNAs in dendrites of neurons to assay the evolutionary differences in subcellular dendritic transcripts localization. To assess neuronal dendrite expression divergence between mice and rats, we used the Affymetrix array platform to assay the transcriptomes of micro-dissected individual dendrites of hippocampal neurons in dispersed primary cell cultures from Sprague-Dawley rat (9 biological replicates), C57BL/6 mouse (14 biological replicates), and Balb/c mouse (5 biological replicates)
2014-10-14 | E-GEOD-61082 | biostudies-arrayexpress
Project description:Using microdissected dendrites from primary cultures of hippocampal neurons of two mouse strains (C57BL/6 and Balb/c) and one rat strain (Sprague-Dawley), we investigate via microarrays, subcellular localization of mRNAs in dendrites of neurons to assay the evolutionary differences in subcellular dendritic transcripts localization. To assess neuronal dendrite expression divergence between mice and rats, we used the Affymetrix array platform to assay the transcriptomes of micro-dissected individual dendrites of hippocampal neurons in dispersed primary cell cultures from Sprague-Dawley rat (9 biological replicates), C57BL/6 mouse (14 biological replicates), and Balb/c mouse (5 biological replicates)
2014-10-14 | E-GEOD-61083 | biostudies-arrayexpress
Project description:Using microdissected dendrites from primary cultures of hippocampal neurons of two mouse strains (C57BL/6 and Balb/c) and one rat strain (Sprague-Dawley), we investigate via microarrays, subcellular localization of mRNAs in dendrites of neurons to assay the evolutionary differences in subcellular dendritic transcripts localization.
2014-10-14 | GSE61083 | GEO
Project description:Using microdissected dendrites from primary cultures of hippocampal neurons of two mouse strains (C57BL/6 and Balb/c) and one rat strain (Sprague-Dawley), we investigate via microarrays, subcellular localization of mRNAs in dendrites of neurons to assay the evolutionary differences in subcellular dendritic transcripts localization.
2014-10-14 | GSE61082 | GEO
Project description:BACKGROUND:RNA localization involves cis-motifs that are recognized by RNA-binding proteins (RBP), which then mediate localization to specific sub-cellular compartments. RNA localization is critical for many different cell functions, e.g., in neuronal dendrites, localization is a critical step for long-lasting synaptic potentiation. However, there is little consensus regarding which RNAs are localized and the role of alternative isoforms in localization. A comprehensive catalog of localized RNA can help dissect RBP/RNA interactions and localization motifs. Here, we utilize a single cell sub-cellular RNA sequencing approach to profile differentially localized RNAs from individual cells across multiple single cells to help identify a consistent set of localized RNA in mouse neurons. RESULTS:Using independent RNA sequencing from soma and dendrites of the same neuron, we deeply profiled the sub-cellular transcriptomes to assess the extent and variability of dendritic RNA localization in individual hippocampal neurons, including an assessment of differential localization of alternative 3'UTR isoforms. We identified 2225 dendritic RNAs, including 298 cases of 3'UTR isoform-specific localization. We extensively analyzed the localized RNAs for potential localization motifs, finding that B1 and B2 SINE elements are up to 5.7 times more abundant in localized RNA 3'UTRs than non-localized, and also functionally characterized the localized RNAs using protein structure analysis. CONCLUSION:We integrate our list of localized RNAs with the literature to provide a comprehensive list of known dendritically localized RNAs as a resource. This catalog of transcripts, including differentially localized isoforms and computationally hypothesized localization motifs, will help investigators further dissect the genome-scale mechanism of RNA localization.
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Project description:Proteostasis at neuronal projections supports the molecular basis behind long-term information storage and movement control. It is maintained through regulated protein synthesis and degradation and chaperone-assisted protein folding. Using high-resolution fluorescent microscopy, we discovered that neurons localize a subset of chaperone mRNAs to their dendrites and increase this asymmetric localization following proteotoxic stress. The most abundant chaperone mRNA in dendrites encodes for the constitutive heat shock protein 70, HSPA8. Most Hspa8 mRNAs travel in dendrites as single molecules. In the dendrites, Hspa8 mRNAs are locally translated by mono and polyribosomes, and proteotoxic stress further enhances the percentage of mRNAs engaged in translation and their efficiency. We discovered that Fused in Sarcoma (FUS) and heterogenous nuclear ribonucleoprotein A2/B1 (HNRNPA2B1) participate in stress-mediated localization of Hspa8 mRNA in dendrites of mouse and human motor neurons, respectively. As such, FUS knocked down neurons accumulate misfolded proteins in dendrites upon stress exposure. Together, these results reveal a novel mechanism allowing neurons to uphold proteostasis at dendrites and spines upon stress.
2024-11-13 | PXD046036 | Pride
Project description:To study the correlation between mRNA stability and subcellular mRNA localisation we globally interferred with mRNA degradation in primary cortical neurons by overexpressing a catalytic mutant of deadenylase CAF1 that functions as a dominant negative form. Neurons were separated into subcellular compartments (neurite, soma-cytoplasm and nucleus) and sequenced in parallel with respective compartments from GFP- expressing control neuons.
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