Whole animal RNA Seq of wild type and RBP/TF mutants

Gene 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 in C. 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-1 and tdp-1, and the homeodomain TF ceh-14. Losing any one of these genes alone has no significant effect on the health of the organism. However, fust-1; ceh-14 and tdp-1; ceh-14 double 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 identifies ceh-14 as the main controller of transcript levels, while fust-1 and tdp-1 control splicing through a shared role in exon inhibition. We identify a cassette exon in the polyglutamine-repeat protein pqn-41 which tdp-1 inhibits. Loss of tdp-1 causes the pqn-41 exon to be aberrantly included, and forced skipping of this exon in tdp-1; ceh-14 double mutants rescues fertility. Together our findings identify a novel shared physiological role for fust-1 and tdp-1 in promoting C. elegans fertility in a ceh-14 mutant background and reveal a shared molecular function of fust-1 and tdp-1 in exon inhibition. Biological triplicates of wild-type, TF mutant (ceh-14), two RBP mutants (fust-1 and tdp-1) and pairwise TF-RBP combinations