How PRPF31 haplo-deficiency, as a general splicing factor is associated with retina specific disease, remains unclear. In this study, we investigated the functional splicing effects of PRPF31 downregulation in a model of Human Organotypic Retinal Culture using RNA sequencing technique.

Human eyes from young donors (20-40 years old) were obtained within the 24 hours post mortem from Iranian eye bank. The retinas were isolated and transfected using PRPF31 and scramble siRNA. PRPF31 down regulation was confirmed by quantitative real time PCR (qPCR). The mRNA libraries were paired-end sequenced on Illumina HiSeq 4000 and subsequently analyzed using bioinformatics tools. QRT-PCR for some selected down-regulated genes performed to double check the results.

PRPF31 depletion in siRNA treated samples led to down-regulation of 2% of genes and up-regulation of 1.5% of genes, as a whole. These differentially down-regulated genes are enriched to photo-transduction pathway (RHO, GUCA, PDEG, SAG). In addition, enrichment analysis for gene ontology revealed ATP-sensitive potassium channel complex and rhodopsin mediated signaling pathways involvement. Interestingly, transcription-coupled splicing is significantly increased in PRPF31 depleted samples, suggesting a compensatory mechanism for splicing reduction. RNA sequencing analysis confirmed QRT-PCR results of selected genes involved in photo-transduction.

Our data reveals PRPF31 deficiency has a crucial role in retina specific pathology by affecting the expression of wide range of genes implicated in photo-transduction and rhodopsin mediated signaling pathway, as its major splicing function.