Nova regulates brain-specific splicing to shape the synapse

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.

PQBP1, a factor linked to intellectual disability, affects alternative splicing associated with neurite outgrowth

“…6C; Supplemental Table S4). The GO term enrichment profile for PQBP1's AS targets is specific compared with high-throughput studies on other proteins in neurons, especially RNA splicing, chromatin modification, dendrite development-related functions, and ARF signal transduction (Ule et al 2005;Gehman et al 2011;Charizanis et al 2012). Bcl-x AS is not conserved from humans to mice and was not identified as a target in this analysis.…”

Control of alternative pre-mRNA splicing by Ca++ signals

“…Hopefully, the now available mammalian RNAi libraries could also be applied for functional screening of genes essential in inducible alternative splicing. Thirdly, splicing-sensitive microarrays and whole genome exon arrays [64,78,82,83,[223][224][225], combined with loss-of-functions of splicing factors (such as knockout or RNAi), will allow the identification of a group of exons/genes controlled by a particular factor during Ca ++ -regulation of splicing. Lastly, bioinformatics approaches with highly predictive RNA elements could also help identify a group of exons regulated by Ca ++ signals, as has been demonstrated for the alternative splicing factor Nova-1 [62].…”

“…The relative levels of positive and negative regulatory factors determine the generation of variant mRNA isoforms in specific cell types [73][74][75]. Brainenriched splicing factors include Nova-1 and -2 [62][63][64][65][66], FOX-1 and -2 [54-61], PTBP2 (nPTB) and neuronal Hu proteins [76][77][78][79][80][81][82][83].…”

L’épissage des ARN pré-messagers : quand le splicéosome perd pied

“…Figure 1B). Certains membres d'une même famille peuvent parfois pré-senter des spécificités d'expression tissulaire marquées comme, par exemple, les protéines NOVA enrichies au niveau du cerveau [6]. De fait, les prédictions informatiques de la position des sites d'activité des protéines SR et hnRNP sont sensiblement moins performantes que celles des sites consensus évoqués plus haut.…”