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3' mRNA-seq of neurites and soma isolated from mESC-derived neurons

ABSTRACT: 3' mRNA-seq of neurites and soma isolated from mESC-derived neurons

PROVIDER: PRJEB28860 | ENA |

REPOSITORIES: ENA

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3' mRNA-seq of neurites and soma isolated from mESC-derived neurons

Project description:3' mRNA-seq was performed with QuantSeq 3' mRNA-Seq kit (Lexogen 015) according to the manufacturer’s recommendations. 3' mRNA-seq was done in biological triplicates (soma) or duplicates (neurites), using 260 ng of total RNA from neurites or soma of mESC-derived neurons per sample. Libraries were pooled and sequenced on Illumina NextSeq 500 system with a single-end 150-cycle run.

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Localization of functionally distinct CDC42 isoforms in neurons requires alternative 3'UTR usage

Project description:The proper subcellular localization of RNAs and local translational regulation is crucial in highly compartmentalized cells, such as neurons. RNA localization is mediated by specific cis-regulatory elements usually found in mRNA 3'UTRs. Therefore, processes that generate alternative 3'UTRs – alternative splicing and polyadenylation – have the potential to diversify mRNA localization patterns in neurons. Here, we performed mapping of alternative 3'UTRs in neurites and soma isolated from mESC-derived neurons. Our analysis identified 593 genes with differentially localized 3'UTR isoforms. In particular, we have shown that two isoforms of Cdc42 gene with distinct functions in neuronal polarity are differentially localized between neurites and soma of mESC-derived and mouse primary cortical neurons, at both mRNA and protein level. Using reporter assays and 3'UTR swapping experiments, we have identified the role of alternative 3’UTRs and mRNA transport in differential localization of alternative CDC42 protein isoforms. Moreover, we used SILAC to identify isoform-specific Cdc42 3'UTR-bound proteome with potential role in Cdc42 localization and translation. Our analysis points to usage of alternative 3'UTR isoforms as a novel mechanism to provide for differential localization of functionally diverse alternative protein isoforms.

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Expression data from Soma dissected from single-cell rat Hippocampal neurons

2014-10-14 | GSE61085 | GEO

Expression data from Soma dissected from single-cell mouse Hippocampal neurons

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CRISPR-Mediated Knockout of Long 3' UTR mRNA Isoforms in mESC-Derived Neurons.

Project description: Not available

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Profiling of soma and neurite transcriptomes

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