Multiple transcripts of sodium channel SCN8A (NaV1.6) with alternative 5′- and 3′-untranslated regions and initial characterization of the SCN8A promoter

To identify the transcriptional start sites of the neuronal channel SCN8A, we carried out 5′-RACE (rapid amplification of cDNA ends) with RNA from human and mouse brain. We recovered four mutually exclusive 5′-untranslated exons (exon 1a to exon 1d) that map to a 1.8-kb region of genomic DNA located ∼70 kb upstream of the first coding exon. The same 5′-untranslated exons are expressed in central, peripheral and sympathetic nervous system and in embryonic and adult brain. A 4.8-kb genomic fragment containing these 5′ exons demonstrated promoter activity in transfected MN-1 cells. In transgenic mice, transcription of the 4.8-kb promoter was restricted to brain and spinal cord. The 4.8-kb promoter contains eight consensus Sp1-binding sites and two Inr sites. A potential NRSE/RE-1 site is located nearby. Two active polyadenylation sites identified by 3′-RACE are conserved in human, mouse, and chicken SCN8A. Sequence comparison of human and mouse SCN8A identified 12 conserved noncoding elements whose effect on transcription was tested in transfected cells.