Systematic name M1551
Brief description Genes whose splicing in neocortex was most affected by knock out of NOVA2 [GeneID=4858].
Full description or abstract Alternative RNA splicing greatly increases proteome diversity and may thereby contribute to tissue-specific functions. We carried out genome-wide quantitative analysis of alternative splicing using a custom Affymetrix microarray to assess the role of the neuronal splicing factor Nova in the brain. We used a stringent algorithm to identify 591 exons that were differentially spliced in the brain relative to immune tissues, and 6.6% of these showed major splicing defects in the neocortex of Nova2-/- mice. We tested 49 exons with the largest predicted Nova-dependent splicing changes and validated all 49 by RT-PCR. We analyzed the encoded proteins and found that all those with defined brain functions acted in the synapse (34 of 40, including neurotransmitter receptors, cation channels, adhesion and scaffold proteins) or in axon guidance (8 of 40). Moreover, of the 35 proteins with known interaction partners, 74% (26) interact with each other. Validating a large set of Nova RNA targets has led us to identify a multi-tiered network in which Nova regulates the exon content of RNAs encoding proteins that interact in the synapse.
Collection C2: curated gene sets
      CGP: chemical and genetic perturbations
Source publication Pubmed 16041372   Authors: Ule J,Ule A,Spencer J,Williams A,Hu JS,Cline M,Wang H,Clark T,Fraser C,Ruggiu M,Zeeberg BR,Kane D,Weinstein JN,Blume J,Darnell RB
Exact source Table 1
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Organism Mus musculus
Contributed by John Newman (University of Washington)
Source platform MOUSE_GENE_SYMBOL
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Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
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Version history 3.1: First introduced

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