The splicing kinase PRPF-4 is required for somatic development and germline function in C. elegans

Abstract

Pre-mRNA splicing is essential for gene expression, yet how disruption of core spliceosomal factors produces tissue- and developmental stage-specific phenotypes remains poorly understood. Here, we investigated the in vivo function of the conserved spliceosomal kinase PRPF-4 in C. elegans using endogenous reporter analysis, conditional protein depletion, and transcriptome-wide analysis of alternative splicing and gene expression. We found that PRPF-4 is broadly expressed throughout development and is continuously required for postembryonic development, with distinct requirements in the pharynx, nervous system, and germline. Acute PRPF-4 depletion rapidly disrupts alternative splicing across thousands of transcripts, with exon skipping representing the predominant class of affected events. In addition, PRPF-4 depletion results in a robust transcriptome shift with induction of components of the spliceosome and repression of ciliary and ion transport-related transcripts. These findings establish PRPF-4 as a central regulator of RNA metabolism and demonstrate the far-reaching effects on gene expression caused by loss of core spliceosomal components. Author Summary Pre-mRNA splicing, a process in which newly synthesized RNA molecules are cut and joined to produce mature RNA molecules, is one of the most fundamental processes required for life, and defects in splicing have been linked to many human diseases. To understand why defects in proteins that control splicing can affect different tissues and stages of development in different ways, we studied a conserved splicing protein called PRPF-4 in the nematode C. elegans. We found that PRPF-4 is widely present throughout development and is continuously required for normal development after embryogenesis, with particularly important roles in the pharynx, nervous system, and germline. Removing PRPF-4 causes numerous splicing errors and changes the levels of many gene transcripts, including increased levels of transcripts involved in RNA splicing and decreased levels of transcripts involved in cilia and ion transport. Our findings demonstrate that PRPF-4 is an essential regulator of RNA processing and show that disruption of the splicing machinery can lead to diverse developmental and tissue-specific phenotypes.