TDP-1 and FUST-1 co-inhibit exon inclusion and control fertility together with transcriptional regulation

Abstract

ABSTRACTGene expression is a multistep, carefully controlled process, and crosstalk between regulatory layers plays an important role in coordinating gene expression. To identify functionally relevant coordination between transcriptional and post-transcriptional gene regulation, we performed a systematic reverse-genetic interaction screen inC. elegans. We combined RNA binding protein (RBP) and transcription factor (TF) mutants, creating over 100 RBP; TF double mutants. This screen identified a variety of unexpected double mutant phenotypes, including two strong genetic interactions between the ALS-related RBPs,fust-1andtdp-1, and the homeodomain TFceh-14. Losing any one of these genes alone has no significant effect on the health of the organism. However,fust-1; ceh-14andtdp-1; ceh-14double mutants both exhibit strong temperature-sensitive fertility defects. Both double mutants exhibit defects in gonad morphology, sperm function, and oocyte function. RNA-seq analysis of double mutants identifiesceh-14as the main controller of transcript levels, whilefust-1andtdp-1control splicing through a shared role in exon inhibition. We identify a cassette exon in the polyglutamine-repeat proteinpqn-41whichtdp-1inhibits. Loss oftdp-1causes thepqn-41exon to be aberrantly included, and forced skipping of this exon intdp-1; ceh-14double mutants rescues fertility. Together our findings identify a novel shared physiological role forfust-1andtdp-1in promotingC. elegansfertility in aceh-14mutant background and reveal a shared molecular function offust-1andtdp-1in exon inhibition.