Identification and copy number variant analysis of enhancer regions of genes causing spinocerebellar ataxia

Currently, routine diagnostics for spinocerebellar ataxia (SCA) consist of analyses that look for polyQ repeat expansions and conventional variations affecting the proteins encoded by known SCA genes. Despite all the effort, [~]40% of the patients still remain without a genetic diagnosis after routine tests. Increasing evidence suggests that variations in the enhancer regions of genes involved in neurodegenerative disorders can also be disease-causing. Since the enhancers of SCA genes are not yet known, it remains to be determined whether variations in these regions are a cause of SCA. In this pilot project, we aimed to identify the enhancers of the SCA genes ATXN1, ATXN3, TBP and ITPR1 in human cerebellum using 4C-seq experiments, publicly available datasets, reciprocal 4C-seq and luciferase assays. We then screened these enhancers for copy number variants (CNVs) in a cohort of genetically undiagnosed SCA patients. We identified two active enhancers for each of the four SCA genes in human cerebellar tissue. In addition, for TBP and ITPR1, we observed interactions between the putative enhancers of each gene. CNV analysis did not reveal any CNVs in the active enhancers of the four SCA genes in any of the genetically undiagnosed SCA patients. However, in one patient, we noted a CNV deletion with unknown clinical significance near one of the active enhancers of ITPR1. These results not only reveal elements involved in regulation of SCA genes, they can also lead to the discovery of novel SCA-causing genetic variants. As enhancer variations are increasingly recognized to cause brain disorders, screening the enhancers of ATXN1, ATXN3, TBP and ITPR1 for variations other than CNVs and identifying and screening enhancers of other SCA genes might elucidate the genetic cause in genetically undiagnosed patients.