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Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons

By Yuan Yuan, Shirley Xie, Robert B. Darnell, Andrew J Darnell, Yuhki Saito, Hemali Phatnani, Elisabeth Murphy, Chaolin Zhang, Tom Maniatis, Robert B. Darnell

Posted 07 Jan 2018
bioRxiv DOI: 10.1101/237347 (published DOI: 10.1186/s13059-018-1493-2)

Background: Alternative RNA processing plays an essential role in shaping cell identity and connectivity in the central nervous system (CNS). This is believed to involve differential regulation of RNA processing in various cell types. However, in vivo study of cell-type specific post-transcriptional regulation has been a challenge. Here, we developed a sensitive and stringent method combining genetics and CLIP (crosslinking and immunoprecipitation) to globally identify regulatory interactions between NOVA and RNA in the mouse spinal cord motoneurons (MNs). Results: We developed a means of undertaking MN-specific CLIP to explore MN-specific protein-RNA interactions relative to studies of the whole spinal cord. This allowed us to pinpoint differential RNA regulation specific to MNs, revealing major role for NOVA in regulating cytoskeleton interactions in MNs. In particular, NOVA specifically promotes the palmitoylated isoform of a cytoskeleton protein Septin 8 in MNs, which enhances dendritic arborization. Conclusions: Our study demonstrates that cell type-specific RNA regulation is important for fine-tuning motoneuron physiology, and highlights the value of defining RNA processing regulation at single cell type resolution.

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