Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice

BackgroundGenes with multiple co-active promoters appear common in brain, yet little is known about functional requirements for these potentially redundant genomic regulatory elements.SCN1A,which encodes the NaV1.1 sodium channel alpha subunit, is one such gene with two co-active promoters. Mutations inSCN1Aare associated with epilepsy, including Dravet syndrome (DS). The majority of DS patients harbor coding mutations causingSCN1Ahaploinsufficiency; however, putative causal non-coding promoter mutations have been identified.MethodsTo determine the functional role of one of these potentially redundantScn1apromoters, we focused on the non-codingScn1a1b regulatory region, previously described as a non-canonical alternative transcriptional start site. We generated a transgenic mouse line with deletion of the extended evolutionarily conserved 1b non-coding interval and characterized changes in gene and protein expression, and assessed seizure activity and alterations in behavior.ResultsMice harboring a deletion of the 1b non-coding interval exhibited surprisingly severe reductions ofScn1aand NaV1.1 expression throughout the brain. This was accompanied by electroencephalographic and thermal-evoked seizures, and behavioral deficits.ConclusionsThis work contributes to functional dissection of the regulatory wiring of a major epilepsy risk gene,SCN1A. We identified the 1b region as a critical disease-relevant regulatory element and provide evidence that non-canonical and seemingly redundant promoters can have essential function.