Differential expression of exon 5 splice variants of sodium channel α subunit mRNAs in the developing mouse brain

doi:10.1016/j.neuroscience.2009.12.011

Neuroscience

Volume 166, Issue 1, 10 March 2010, Pages 195-200

https://doi.org/10.1016/j.neuroscience.2009.12.011 Get rights and content

Abstract

Sodium channel α subunit genes expressed in the human brain, SCN1A, SCN2A, SCN3A and SCN8A, are subject to alternative splicing of coding exons 5N and 5A. In this study we examined expression of α subunit mRNA and exon 5 splicing in the developing mouse brain. Expression levels of Scn1a, Scn2a and Scn8a mRNAs increase postnatally, whereas Scn3a mRNA expression levels decrease. Scn1a mRNA contains only exon 5A, due to the absence of exon 5N in the mouse Scn1a gene. At birth, Scn2a is the only sodium channel α subunit mRNA that contains higher or equal amounts of the 5N isoform compared to the 5A isoform in most brain regions. In contrast, the predominant isoform of Scn3a and Scn8a mRNAs in the newborn mouse brain is 5A. 5N/5A ratios for each of the three mRNAs vary across brain regions, with cortex≥hippocampus>thalamus>cerebellum. In all brain regions and for all three α subunits, 5N/5A ratios gradually decrease with age, levelling at a value between 0.1 and 0.2. These findings suggest potential involvement of common factors in the alternative splicing of exon 5 for all three transcripts, and that expression of these factors varies between brain regions and changes during development. Differences in the strength of exon 5N and/or exon 5A splice sites in Scn2a pre-mRNA as compared to Scn1a and Scn8a may underlie the observed differences in 5N/5A ratios in the three α subunit mRNAs.

Section snippets

Tissue collection and RNA extraction

Brains of male C57BL/6J mice were collected at seven postnatal ages (n=3 for each age group) and divided into four regions: cerebellum, thalamus, hippocampus and cortex. All animal experiments conformed to Australian Code of Practice for the Care and Use of Animals for Scientific Purposes, and every effort was taken to reduce the number of animals used and to minimize their suffering. Tissue samples were frozen in liquid nitrogen and stored at −80 °C. Total RNA was extracted from the brain

Relative expression of exon 5 splice variants

In the mouse Scn1a gene, the region corresponding to human exon 5N contains several stop codons and is not flanked by a canonical splice site sequence at the 3′ end (Fig. 1B), suggesting that the “neonatal” Scn1a mRNA is unlikely to be expressed in mice. The 5N and 5A coding exons in mouse Scn2a, Scn3a and Scn8a genes are flanked by canonical splice sites (not shown), suggesting that alternative splicing of exon 5 occurs in the respective pre-mRNAs. All mouse sodium channel α subunit genes

Discussion

In this study we have examined developmental and regional expression of exon 5 splice variants of sodium channel α subunit mRNAs in the mouse brain. The results showed that mouse Scn1a mRNA is expressed only as the 5A isoform, unlike its human ortholog. This result, together with the published data showing a wide range of variability in the proportion of the 5N SCN1A mRNA in adult human population (Heinzen et al., 2007), suggests that the “neonatal” isoform of SCN1A-encoded protein is not

Acknowledgments

We thank Jane Howard and Damian F. J. Purcell for help with agarose gel analysis.

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The “neonatal” 5N exon is enriched in SCN2A transcripts in the embryonic and early postnatal brain (Gazina et al., 2015; Liang et al., 2021). In rodents, 5N inclusion declines postnatally as Scn2a mRNA levels increase, resulting in “adult” exon 5A-containing isoforms encoding the majority of Nav1.2 channels in cortical neurons after the second postnatal week (Gazina et al., 2010, 2015). These splicing dynamics also differ across brain regions in the mouse (Gazina et al., 2010), and different patterns of exon 5A and 5N splicing have been reported in the genes coding for other voltage-gated sodium channel alpha subunits in the mouse and human brain, including the neurodevelopmental disease-associated SCN8A (encoding Nav1.6) (Gazina et al., 2010; Liang et al., 2021).
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In this splice assay, the proband-4- and 5-specific variants (∼250 bp from 20N) did not show any effect on the splicing of 20N, nor did they disrupt the splicing of the junctions between exon 20 and intron 20 or between exon 20 and exon 21 (Figure S3). We propose that the reduced binding of putative cell-specific splicing factors, as described for other sodium channels, might explain the lack of effects in this system.6,22–24 Cell-specific sodium-channel alternative splicing is known to occur for poison exons in SCN1A (20N)21 and SCN8A (18N).6
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Molecular NeuroscienceResearch PaperDifferential expression of exon 5 splice variants of sodium channel α subunit mRNAs in the developing mouse brain

Abstract

Section snippets

Tissue collection and RNA extraction

Relative expression of exon 5 splice variants

Discussion

Acknowledgments

Eur J Pharmacol

J Biol Chem

Am J Hum Genet

Gene

J Biol Chem

Mol Cell Neurosci

Association between SCN1A polymorphism and carbamazepine-resistant epilepsy

Br J Clin Pharmacol

Differential regulation of three sodium channel messenger RNAs in the rat central nervous system during development

EMBO J

Regional and temporal expression of sodium channel messenger RNAs in the rat brain during development

Exp Brain Res

Molecular Neuroscience
Research Paper
Differential expression of exon 5 splice variants of sodium channel α subunit mRNAs in the developing mouse brain