Characterization of 5′ untranslated regions of the voltage-gated sodium channels SCN1A, SCN2A, and SCN3A and identification of cis-conserved noncoding sequences

Abstract

The human voltage-gated sodium channel gene cluster on chromosome 2q24 contains three paralogs, SCN1A, SCN2A, and SCN3A, which are expressed in the central nervous system. Mutations in SCN1A and SCN2A cause several subtypes of idiopathic epilepsy. Furthermore, many SCN1A mutations are predicted to reduce protein levels, emphasizing the importance of precise sodium channel gene regulation. To investigate the genetic factors that regulate the expression of SCN1A, SCN2A, and SCN3A, we characterized the 5' untranslated region of each gene. We identified multiple noncoding exons and observed brain region differences in the expression levels of noncoding exons. Comparative sequence analysis revealed 33 conserved noncoding sequences (CNSs) between the orthologous mammalian genes and 6 CNSs between the three human paralogs. Seven CNSs corresponded to noncoding exons. Twelve CNSs were evaluated for their ability to alter the transcription of a luciferase reporter gene, and 3 resulted in a modest, but statistically significant change.

Identification of the promoter region and the 5′‐untranslated exons of the human voltage‐gated sodium channel Nav1.1 gene (SCN1A) and enhancement of gene expression by the 5′‐untranslated exons

“…The region upstream of the transcription start site of noncoding exon h1u is targeted as a potential location of promoter in the present study, because both the present results from 30 clones and those from 150 clones in a previous report (Martin et al, 2007) suggest that most of the transcripts in human brain are initiated from exon h1u (or similarly 1a by Martin et al, 2007). However, with the PROMO program and the TRANSFAC database, we failed to find the classical transcriptional elements directly upstream of the transcription start site.…”

“…Further investigation will be required to determine the role of each noncoding exon. Because there is increasing interest in the study of the role of noncoding exons in gene expression, but no functional SCN1A promoter has been reported thus far (Martin et al, 2007), our studies suggest that the P 2.7 could be used as a tool to investigate the role of each noncoding exon.…”

“…The voltage-gated sodium channels have complex 5 0 -untranslated regions, and human SCN1A represents the most complex one, with seven noncoding exons distributed over a 75-kb interval upstream of the first coding exon (Martin et al, 2007). This is one of the reasons why the promoter region of human SCN1A has not been identified so far.…”

“…1, 2). Recently, Martin et al (2007) performed 5 0 RACE of SCN1A, SCN2A, and SCN3A with mRNA from the human frontal cortex, cerebellum, and hippocampus and found that the 5 0 - untranslated exons of these genes were alternatively spliced in different brain regions. They also found that the most frequently utilized exon (exon 1a, GenBank accession No.…”

Promoter Analysis of Mouse Scn3a Gene and Regulation of the Promoter Activity by GC Box and CpG Methylation

“…A higher y value indicated higher sequence conservation. The x-axis indicates the distance (base pairs) from the transcription start site (Long et al 2009;Martin et al 2007), we cloned a 1.2-kb fragment (F1.2) around the TSS (−1,049 to +157), which was confirmed to have promoter activity in three cell lines.…”