Nova autoregulation reveals dual functions in neuronal splicing

Abstract

The Nova family of neuron-specific RNA-binding proteins were originally identified as targets in an autoimmune neurologic disease characterized by failure of motor inhibition. Nova-1 regulates alternative splicing of premRNAs encoding the inhibitory neurotransmitter receptor subunits GABA A Rc2 and GlyRa2 by directly binding intronic elements, resulting in enhancement of exon inclusion. Here we identify exon E4 in the Nova-1 pre-mRNA itself, encoding a phosphorylated protein domain, as an additional target of Nova-dependent splicing regulation in the mouse spinal cord. Nova binding to E4 is necessary and sufficient for Nova-dependent exon exclusion. E4 harbors five repeats of the known Nova-binding tetranucleotide YCAY and mutation of these elements destroys Nova-dependent regulation. Furthermore, swapping of the sites from Nova-1 and GABA A Rc2 indicates that the ability of Nova to enhance or repress alternative exon inclusion is dependent on the position of the Nova-binding element within the pre-mRNA. These studies demonstrate that in addition to its previously described role as a splicing activator, Nova autoregulates its own expression by acting as a splicing repressor.

Recent Advances in Understanding of Alternative Splicing in Neuronal Pathogenesis

“…Bioinformatics analysis revealed the mechanism of Nova-mediated alternative splicing regulation (Ule, et al, 2006). Consistent with previous reports using minigene splicing assays, the position of Nova-binding sites in pre-mRNAs determines the effect of Nova proteins on splicing (Dredge, et al, 2005). For a cassette exon, Nova binding to its downstream intronic YCAY clusters enhances exon inclusion, whereas exon skipping occurs when Nova binds either immediately upstream of or within the exon.…”

“…Therefore, Nova can function either as a positive or negative splicing regulator via binding to intronic or exonic YCAY elements. Further study by swapping of Nova-1-binding sites between various splicing substrates of Nova-1 indicated that the action of Nova-1 is determined by the position of the Nova-binding elements (Dredge, et al, 2005). This positional effect has also been found in other splicing regulators (see below).…”

“…Nova-1 was subsequently shown to promote GABA A R2 exon 9 inclusion via a distal downstream intronic YCAY-rich splicing enhancer. Notably, the Nova-1 gene itself harbors five YCAY repeats in its exon 4 that are indeed essential for Nova-1 autoregulation (Dredge, et al, 2005). Inclusion of exon 4 in Nova-1 transcripts was increased in haploinsufficient Nova +/-mice.…”

“…Previous studies have also revealed how Nova proteins may modulate the activity of the spliceosome. For example, Nova binding to exons may interfere with U1 snRNP binding to the 5' splice site, thereby inhibiting splicing (Dredge, et al, 2005). When Nova binds to the downstream intron of a regulated exon, it may facilitate spliceosome assembly and promote exon inclusion (Dredge, et al, 2005).…”

“…For example, Nova binding to exons may interfere with U1 snRNP binding to the 5' splice site, thereby inhibiting splicing (Dredge, et al, 2005). When Nova binds to the downstream intron of a regulated exon, it may facilitate spliceosome assembly and promote exon inclusion (Dredge, et al, 2005). As described above, Nova and Fox proteins may coregulate alternative splicing of a considerable number of transcripts in a cooperative or antagonistic manner (C. Zhang, et al, 2010).…”