Aluinsertion-mediated dsRNA structure formation with pre-existingAluelements as a novel disease-causing mechanism

Abstract

We have recently reported a homozygous Alu insertion variant (termed Alu_Ins) within the 3’-untranslated region (3’-UTR) of the SPINK1 gene as the cause of a new pediatric disease entity. Although Alu-Ins has been shown, by means of a full-length gene expression assay (FLGEA), to result in the complete loss of SPINK1 mRNA expression, the precise underlying mechanism(s) has remained elusive. Herein, we filled this knowledge gap by adopting a hypothesis-driven approach. Employing RepeatMasker, we identified two Alu elements (termed Alu1 and Alu2) within the SPINK1 locus; both are located deep within intron 3 and, most importantly, reside in the opposite orientation to Alu-Ins. Using FLGEA, we provide convincing evidence that Alu-Ins disrupts splicing by forming RNA secondary structures with Alu1 in the pre-mRNA sequence. Our findings reveal a previously undescribed disease-causing mechanism, resulting from an Alu insertion variant, which has implications for Alu detection and interpretation in human disease genes.

Long-read technologies identify a hidden inverted duplication in a family with choroideremia

“… 60 , 61 , 62 , 63 In a recent study, Masson et al. 64 investigated the disease-causing mechanism of an Alu -element insertion in the 3′ UTR of the gene SPINK1 . By a full-gene expression assay, they confirmed that the inserted Alu element is in the opposite orientation with an existing Alu element in SPINK1 intron 3, which disrupted splicing by forming an altered RNA secondary structure leading to severe infantile isolated exocrine pancreatic insufficiency.…”