Identification of UAP56 and DYRK1A as the splicing regulatory proteins in Spinal Muscular Atrophy

Abstract

Alternative splicing (AS) produces various mRNA isoforms in human. Spinal Muscular Atrophy (SMA) is a recessive genetic disease in which SMN1 gene is deleted or mutated. Although SMN2 gene, a duplicate of SMN2, still exist is SMA patients, mutations in SMN2 cause the production of significantly less amounts of cassette exon included isoform than SMN1, so that less functional SMN protein are made. In this study, I identified UAP56 and Dyrk1A as the essential regulatory proteins for AS of SMN2 pre-mRNA. I found that knocking-down (KD) of both UAP56 and Dyrk1A stimulate cassette exon inclusion of SMN2 pre-mRNA significantly. To further explore the AS targets of these two proteins, I applied RASL-seq technology by using UAP56 KD cells, and rMATs analysis from the RNA-seq results with Dyrk1A KD cells that were downloaded from database. I discovered four enhanced cassette exon and three repressed cassette exon alternative splicing (AS) events in UAP56 knockdown (KD) cells. Utilizing functional analysis with DAVID, I observed that in the upregulated genes, mRNA processing and mRNA splicing played a significant role. Conversely, in the downregulated genes, functions were primarily associated with positive regulation of transcription, DNA-templated, and RNA splicing, with these functions being linked to UAP56. In addition, I also found 367 of cassette exon enhanced and 367 of cassette exon repressed AS events in Dyrk1A KD cells. The upregulated genes are mainly involved in positive regulation of transcription from RNA polymerase 2 promoter and cell differentiation, while the downregulated genes are primarily associated with xenobiotic metabolic processes. I discovered that Dyrk1A modulates SMN2 splicing through SRSF1. In summary, UAP56 and Dyrk1A emerged as key regulators of SMN2 alternative splicing, offering potential insights for SMA treatment.