An RNA Switch of a Large Exon of Ninein Is Regulated by the Neural Stem Cell Specific-RNA Binding Protein, Qki5

International Journal of Molecular Sciences
Yoshika Hayakawa-Yano, Masato Yano

Abstract

A set of tissue-specific splicing factors are thought to govern alternative splicing events during neural progenitor cell (NPC)-to-neuron transition by regulating neuron-specific exons. Here, we propose one such factor, RNA-binding protein Quaking 5 (Qki5), which is specifically expressed in the early embryonic neural stem cells. We performed mRNA-SEQ (Sequence) analysis using mRNAs obtained by developing cerebral cortices in Qk (Quaking) conditional knockout (cKO) mice. As expected, we found a large number of alternative splicing changes between control and conditional knockouts relative to changes in transcript levels. DAVID (The Database for Annotation, Visualization and Integrated Discovery) and Metascape analyses suggested that the affected spliced genes are involved in axon development and microtubule-based processes. Among these, the mRNA coding for the Ninein protein is listed as one of Qki protein-dependent alternative splicing targets. Interestingly, this exon encodes a very long polypeptide (2121 nt), and has been previously defined as a dynamic RNA switch during the NPC-to-neuron transition. Additionally, we validated that the regulation of this large exon is consistent with the Qki5-dependent alternative exon inclu...Continue Reading

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Citations

Sep 26, 2019·Cell Death and Differentiation·Siraj K ZahrFreda D Miller

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Datasets Mentioned

BETA
GSE123927
GSE103248

Methods Mentioned

BETA
PCR
HITS-CLIP

Software Mentioned

CLIP
DAVID ( The Database for Annotation , Visualization and Integr...
OLego
Quantas
HITS
Metascape
EdgeR
DAVID

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