Neuronal proteins custom designed by alternative splicing
Section snippets
Introduction: custom tuned proteins for fine control
Recent analyses suggest that at least 75% of multi-exon genes (see glossary) in the human genome are subject to alternative splicing (see glossary) [1]. This form of pre-mRNA post-transcriptional modification has the potential to expand the proteome exponentially, generating a spectrum of activities (Figure 1). Some genes generate tens of thousands of functionally distinct proteins [2]. Exon choice can vary with cell-type, stage of development, and activity. Alternatively spliced exons that
Molecular diversity on a large scale
Drosophila exhibit one of the most extreme examples of protein diversity to arise from alternative splicing. The DSCAM gene encodes a cell adhesion molecule (Down syndrome cell adhesion molecule) essential for defining axonal guidance in both embryonic and adult flies. The highly variable domains among DSCAM isoforms originate from the combinatorial arrangements of alternatively spliced exons selected primarily from three loci. Theoretically, alternative splicing can generate 38 016 distinct
Finding functional isoforms
There is an abundance of mRNAs in the mammalian brain that contain discrete regions of sequence variation but not all are produced from bona fide splicing and not all are functional. Functionally relevant splice isoforms are expressed at significant levels in a specific tissue, cell-type, or during a particular stage of development. Recent studies have, therefore, focused on the role of specific ion channel splice isoforms in identified neurons with defined functions [7, 8].
Cell-specific expression of ion channel splice isoforms
Perhaps the best demonstration that alternative splicing of ion channel pre-mRNAs can regulate neuronal function comes from studies of calcium activated-potassium channels (Slo) in chicken cochlea. Here, the pattern of alternative splicing of Slo transcripts closely follows the tonotopic map of hair cell tuning along the basilar membrane [9]. This remarkable correlation between the expression of splice isoforms of Slo and the tuning frequency in hair cells shows that alternative splicing can
Alternative splicing modifies synaptic strength
An essential feature of adaptive, complex nervous systems is their capacity to modify neuronal output as sensory input changes. Modifications in ion channel and neurotransmitter receptor functions underlie adaptive changes in neuronal excitability and synaptic efficacy. There are numerous, recent examples of changes in alternative splicing of ion channels and synaptic proteins during development: voltage-gated CaV2 calcium channels [10, 13], synaptosomal protein 25 kDa (SNAP-25) [14],
Activity modifies alternative splicing of synaptic mRNAs
Alternative splicing also represents an attractive mechanism for modifying protein function in neurons after changes in activity. Ehlers and co-workers [22••] provided compelling evidence that alternative splicing of the NMDA receptor drives bidirectional modification of synaptic strength, as neuronal activity is turned up or down. These authors initially showed that NMDA receptor accumulation is controlled at the level of its export from the endoplasmic reticulum (ER) to the plasma membrane,
Orchestrating splicing in select tissues and cells
Above, I cite examples that illustrate dynamic changes in alternative splicing of individual genes. However, studies of those factors that regulate alternative splicing address how this process underlies coordinated changes in the expression of splice isoforms from multiple genes, which collectively control neuronal function and cell phenotype [24••, 25••, 26•].
Coordinated alternative splicing in genes that mediate inhibition
Nova proteins were the first mammalian tissue-specific splicing factors to be identified. They are restricted to the nervous system and are mutated in the human disease paraneoplastic opsoclonus myoclonus ataxia (POMA). Building on these observations, Darnell and co-workers [25••] undertook an unbiased screen of RNAs that bound Nova. They used ultraviolet cross-linking and subsequent immuno-precipitation of protein–RNA complexes to identify several Nova interacting RNAs. Significantly, they
Common proteins involved in highly specialized tasks
While the search for tissue-specific splicing factors continues, a recent report from Fu and co-workers suggests that splicing factors common to many tissues that control constitutive exon splicing can also control alternative splicing [24••]. Members of serine and arginine (SR)-rich splicing factors were first identified as important for constitutive splicing, and are now implicated in other aspects of RNA processing. A conditional gene targeting strategy was used to investigate the functional
Splicing and disease severity
There are a growing number of examples of splicing defects underlying human disease. Splicing can also have a role in modifying disease severity. For example, Timothy syndrome is a novel disorder characterized by multi-organ dysfunction including lethal arrhythmias, webbing of fingers and toes, and autism [27••]. This syndrome results from a de novo mis-sense mutation G406R in the L-type CaV1.2 gene. Notably, the mutation is located in only one of a pair of mutually exclusive exons that encode
Conclusions
Alternative splicing optimizes the activity of key neuronal proteins. Cell-specific inclusion of exons can introduce new sites of interaction that redirect protein targeting. Subtle modifications in the activity of ion channels and receptors can also support gradual changes in neuronal excitability that, for example, might underlie homeostatic plasticity. Currently, we know only a few of the trans-acting splice factors that must control alternative splicing of synaptic protein pre-mRNAs. Future
References and recommended reading
Papers of particular interest, published within the annual period of review, have been highlighted as:
• of special interest
•• of outstanding interest
Glossary
- Alternative splicing
- Most eukaryotic genes consist of several discontinuous coding sequences (exons) separated by non-coding sequences (introns). The initial step in transcription involves production of a pre-messenger RNA that represents a copy of the gene and contains exons and introns. This pre-messenger RNA undergoes several forms of processing that include a step called splicing. Introns are removed and exons are spliced together to form messenger RNA. Certain exons are present in all
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