Dissecting Interactions Across Gene Regulatory Layers in C. elegans

The nematode Caenorhabditis elegans is a powerful tool for studying nervous system genetics. Though relatively simple compared to mammals, C. elegans boasts a remarkably well-conserved neuronal genome and proteome, and its utility in the characterization of neuronal genes has been well-established. However, gene expression is often controlled by complex interactions between multiple genes, and teasing apart the functions of individual genes within such networks remains a challenge. Dissecting these interaction networks is crucial in determining the multifaceted functions of important, conserved regulatory genes. Here we explore interactions between gene regulatory layers in the C. elegans nervous system, employing a synthetic genetic interaction (SGI) screen to identify interactions. In Chapter 1, conservation of Stomatin domain genes in sensory neurons of C. elegans and mice was investigated. We identify a novel conserved role of Stoml3/mec-2 in olfaction, asserting the high conservation of C. elegans neuronal genes. In Chapter 2, we characterize an alternative splicing event in the neuronal kinase sad-1. We find complex coordination between a set of transcription factors and a set of RNA binding proteins that together control alternative isoforms of sad-1 in different neuron types. This prompted us to further investigate widespread coordination between neuronal TFs and RBPs. In Chapter 3, we embarked on a genetic interaction screen with the goal of identifying functionally-relevant interactions between neuronally-enriched TFs and RBPs. We discovered a variety of genetic interactions which suggest novel roles for several TFs and RBPs. Most intriguing, we describe a novel role for two ALS-related RBPs, tdp-1 and fust-1, in facilitating C. elegans fertility. tdp-1 and fust-1 mutants do not exhibit a strong phenotype, but tdp-1; ceh-14 and fust-1; ceh-14 double mutants present a striking loss of fertility, coinciding with a decline in gamete functionality and apparent defects in gonad development. 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. In sum, using a systematic combinatorial genetic interaction screen, we 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. Together, these results highlight the importance of dissecting interaction networks to elucidate functions of individual genes