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

Abstract

Background Genes 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 in SCN1A are associated with epilepsy, including Dravet syndrome (DS). The majority of DS patients harbor coding mutations causing SCN1A haploinsufficiency; however, putative causal non-coding promoter mutations have been identified. Methods To determine the functional role of one of these potentially redundant Scn1a promoters, we focused on the non-coding Scn1a 1b 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. Results Mice harboring a deletion of the 1b non-coding interval exhibited surprisingly severe reductions of Scn1a and NaV1.1 expression throughout the brain. This was accompanied by electroencephalographic and thermal-evoked seizures, and behavioral deficits. Conclusions This 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.

Genome-Wide Meta-Analysis Identifies Two Novel Risk Loci for Epilepsy

“…Interestingly, TTC21B resides in the 2q24.3 locus, a region that contains the wellcharacterized epilepsy risk gene SCN1A (Claes et al, 2001(Claes et al, , 2009Meng et al, 2013;Parihar and Ganesh, 2013;International League Against Epilepsy Consortium on Complex Epilepsies, 2014;Haigh et al, 2021). Although the genome-wide association signal (Figure 2A) and previous studies (Claes et al, 2001(Claes et al, , 2009Meng et al, 2013;Parihar and Ganesh, 2013;International League Against Epilepsy Consortium on Complex Epilepsies, 2014;Haigh et al, 2021) have clearly showed that SCN1A represents the most possible causal gene for this risk locus, our TWAS suggested that TTC21B may also have a potential role in epilepsy (Figure 4). In fact, previous studies also have revealed the potential role of TTC21B in epilepsy (Mirza et al, 2017; The International League Against Epilepsy Consortium on Complex Epilepsies, 2018).…”

Developmental Exposure to a Human-Relevant Polychlorinated Biphenyl Mixture Causes Behavioral Phenotypes That Vary by Sex and Genotype in Juvenile Mice Expressing Human Mutations That Modulate Neuronal Calcium

“…Self-grooming is typical behavior for mice that can be leveraged as a behavioral assay for measuring abnormal repetitive or stereotypic behavior. If mice groom for a significantly longer duration than what is considered typical, it is suggestive of repetitive behavior and this has been characterized in multiple mouse models of neurodevelopmental disorders ( Ey et al, 2011 ; Ellegood et al, 2021 ; Haigh et al, 2021 ). Developmental exposure to the lowest dose of the MARBLES mix (0.1 mg/kg/d) caused a significant increase in time spent grooming in WT male mice ( Figure 2A ).…”

“…Empty cage observations were conducted from P25-P30 as previously described ( Ellegood et al, 2021 ; Haigh et al, 2021 ). Home cages were moved into the behavioral testing room (lux level 110) and allowed at least 1 h to acclimate prior to testing.…”

3D genomics and its applications in precision medicine

“…In the process of studying the spatial structure of the three-dimensional genome and its influence on the transcriptional regulation of different genes, it is necessary to integrate other different types of omics data to define and annotate different elements in the whole genome. Only by combining the biological processes of temporal and spatial dynamics can scientists accurately and deeply carry out the next step in the interpretation of the relationship between gene interaction and function [ 95 ]. Zhao et al.…”