Role of the pre-mRNA processing factor 40 homolog B (PRPF40B) as a transcription factor in neuroblastoma cells

Abstract

PRPF40B is one of the two putative mammalian orthologs of the yeast splicing factor Prp40, which is an essential U1 small nuclear ribonucleoproteinsassociated protein. PRPF40B shows a modular structure containing two WW domains and six FF domains and is highly expressed in brain tissues as well as in neuronal cell lines. PRPF40B has been implicated in the pathogenesis of several neurological disorders, including Huntington disease and Rett syndrome. In order to investigate the role of PRPF40B in nervous cells, we generated two stable PRPF40B-depleted SH-SY5Y cell lines using lentivirusmediated shRNA and CRISPR/Cas9 mediated gene knockout, and performed RNA sequencing of both cell lines. PRPF40B depletion led to widespread alterations in mRNA transcription with minor effects on mRNA processing. Gene set enrichment analysis (GSEA) showed major alterations in the transcription of genes mainly involved in cell calcium transport and homeostasis, cytoskeleton dynamics and synaptic signaling. To better understand the effect of PRPF40B on gene transcription, we used a luciferase reporter assay driven by a minimal promoter with Gal4- PRPF40B and a series of Gal4-PRPF40B deletion mutants.We found that overexpression of PRPF40B inhibits transcription from this minimal promoter and localize the repression region of PRPF40B to the FF domains.