Alternative splicing of the sodium channel SCN8A predicts a truncated two-domain protein in fetal brain and non-neuronal cells

The voltage gated sodium channel alpha subunit SCN8A is one of the most abundant sodium channels in neurons from brain and spinal cord. We have identified two alternatively spliced exons, 18N and 18A, that encode transmembrane segments S3 and S4 in domain III. Exon 18N is expressed in fetal brain and non-neuronal tissues. Transcripts with exon 18N have a conserved in-frame stop codon that predicts the synthesis of a truncated, two-domain protein similar to the fetal form of the muscle calcium channel. The proportion of transcripts containing exon 18N is highest in mouse fetal brain between E12.5 and P1.5; at later ages transcripts containing exon 18A predominate. This developmental program is recapitulated in P19 cells during retinoic acid-induced neuronal differentiation. Non-neuronal tissues contain a low level of SCN8A transcripts containing exon 18N. SCN8A thus provides a new model of differentiation specific splicing. Genomic analysis of SCN8A from human, mouse, and fish demonstrated a conserved structure in which exon 18N is located 300-500 bp upstream of exon 18A. Duplication of exon 18 thus preceded the divergence of fish and mammals. The genomic organization, developmental regulation, and coding content of exons 18N and 18A closely resemble the previously described alternate exons 5N and 5A of the neuronal sodium channel genes. Our proposal that the evolutionary origin of exons 18N and 18A was by duplication of exons 5N and 5A is consistent with other evidence that the four-domain cation channels arose by two rounds of duplication from a single-domain ancestral channel.