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Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons

Sarah A. Middleton, James Eberwine, Junhyong Kim
doi: https://doi.org/10.1101/278648
Sarah A. Middleton
1Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, 160 BRB II/III - 421 Curie Blvd., Philadelphia, PA 19104-6064
4Computational Biology, Target Sciences, GlaxoSmithKline R&D, 1250 S. Collegeville Road Collegeville, PA 19426
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James Eberwine
2Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, 829 BRB II/III, 421 Curie Blvd, Philadelphia PA 19104
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Junhyong Kim
1Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, 160 BRB II/III - 421 Curie Blvd., Philadelphia, PA 19104-6064
3Department of Biology, University of Pennsylvania, 415 S. University Ave, Philadelphia, PA 19104
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Abstract

RNA localization to neuronal dendrites is critical step for long-lasting synaptic potentiation, but there is little consensus regarding which RNAs are localized and the role of alternative isoforms in localization. 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 2,225 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. Finally, we integrate our list of localized RNAs with the literature to provide a comprehensive list of known dendritically localized RNAs as a resource.

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Posted March 07, 2018.
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Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons
Sarah A. Middleton, James Eberwine, Junhyong Kim
bioRxiv 278648; doi: https://doi.org/10.1101/278648
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Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons
Sarah A. Middleton, James Eberwine, Junhyong Kim
bioRxiv 278648; doi: https://doi.org/10.1101/278648

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