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A twin UGUA motif directs the balance between gene isoforms through CFIm and the mTORC1 signaling pathway

ABSTRACT: To identify APA changes in Tsc1-cKO mice, cTag-PAPERCLIP was performed on pAAV-Camk2a-iCre injected Tsc1-WT and Tsc1-floxed cTag-PABP mice. To identify CPSF6-dependent PAS, PAPERCLIP was performed on shCPSF6-BE2C cells with/without doxycycline treatment.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE210768 | GEO | 2022/08/11

REPOSITORIES: GEO

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cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation

Project description:Alternative polyadenylation (APA) is increasingly recognized to regulate gene expression across different cell-types, but obtaining APA maps from individual cell-types typically requires prior purification, a stressful procedure that can itself alter cellular states. Here, we describe a new platform, cTag-PAPERCLIP, that generates APA profiles from single cell populations in intact tissues; cTag-PAPERCLIP requires no tissue dissociation and preserves transcripts in native states. Applying cTag-PAPERCLIP to profile four major cell-types in the mouse brain revealed common APA preferences between excitatory and inhibitory neurons distinct from astrocytes and microglia, regulated in part by neuron-specific RNA-binding proteins NOVA2 and PTBP2. We further identified a role of APA in switching Araf protein isoforms during microglia activation, impacting production of downstream inflammatory cytokines. Our results demonstrate the broad applicability of cTag-PAPERCLIP and a previously undiscovered role of APA in contributing to protein diversity between different cell-types and cellular states within the brain.

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Transcriptomic analysis of cortex tissue from neuron-specific Bmal1 KO mice

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Project description:Alternative polyadenylation (APA) regulates mRNA translation, stability, and protein localization. However, it is unclear to what extent APA regulates these processes uniquely in specific cell types. Using a new technique, cTag-PAPERCLIP, we discovered significant differences in APA between the principal types of mouse cerebellar neurons, the Purkinje and granule cells, as well as between proliferating and differentiated granule cells. Transcripts that differed in APA in these comparisons were enriched in key neuronal functions and many differed in coding sequence in addition to 3’UTR length.

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Project description:cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation

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