Genetic and Epigenetic Regulation of Starvation Resistance in Caenorhabditis elegans

Fluctuations in nutrient availability occur for nearly all species, and adaptation to endure starvation conditions is essential. Genetic pathways involved in regulating starvation resistance are implicated in aging and complex diseases such as cancer, diabetes, and obesity in humans. Consequences of experiencing starvation persist later in life and subsequent generations, suggesting epigenetic regulation. However, much is still unknown about how starvation resistance is regulated and the contributions of different types of regulation. The roundworm Caenorhabditis elegans reversibly arrests development in the absence of food and can endure starvation for several weeks. Here, we investigate how transcriptional, epigenetic, and genetic regulation impact starvation resistance during developmental arrest in C. elegans. Gene expression dynamics change quickly during the first few hours of starvation, and broadly conserved transcription factors are required for starvation survival. However, temporal- and tissue-specific requirements of transcription for supporting starvation survival and recovery are largely unknown. In chapter 2, we used mRNA-seq combined with temporal degradation of RNA Polymerase II in the soma and germline to better understand gene regulation throughout arrest. We find that transcription is required in the soma for survival early in starvation but is dispensable thereafter, and known transcriptional regulators primarily act early in arrest. In contrast, the germline is transcriptionally quiescent throughout starvation, but germline transcripts are relatively stable compared to somatic transcripts. This reveals alternative gene-regulatory strategies in the soma and germline during starvation-induced developmental arrest, with the soma relying on a robust early transcriptional response while the germline relies on mRNA stability to maintain integrity. Phenotypic plasticity is facilitated by epigenetic regulation, and remnants of such regulation may persist after plasticity-inducing cues are gone, even affecting germ cells to impact subsequent generations. However, the relationship between plasticity and transgenerational epigenetic memory is not understood. Dauer diapause provides an opportunity to determine how a plastic response to the early-life environment affects traits later in life and in subsequent generations. In chapter 3, we find that, after extended diapause, postdauer worms initially exhibit reduced reproductive success and greater interindividual variation. In contrast, F3 progeny of postdauers display increased starvation resistance and lifespan, revealing potentially adaptive transgenerational effects. Transgenerational effects are dependent on the duration of diapause, indicating an effect of extended starvation. In agreement, RNA-seq demonstrates a transgenerational effect on nutrient-responsive genes. This work reveals complex effects of nutrient stress over different time scales in an animal that evolved to thrive in feast and famine. Many conserved genes and pathways regulate starvation resistance, but most genetic analysis in C. elegans has been restricted to a single genetic background, potentially restricting identification of additional genes. Hundreds of genetically distinct wild strains of C. elegans have been whole-genome sequenced and can be used for GWAS. In chapters 4 and 5, we implemented two high-throughput sequencing approaches, RAD-seq and MIP-seq, to determine relative starvation resistance of over 100 wild strains over time. We used GWAS to identify QTL associated with starvation resistance, near-isogenic lines to validate QTL, and CRISPR gene editing to modify specific genes within QTL. We focused on genes in the insulin receptor-like domain (irld) family, as this family has been virtually uncharacterized, but the genes share homology with the sole known insulin-like receptor in C. elegans, DAF-2, which is a major regulator of starvation resistance. We found that specific variants in two members of the irld family confers increased starvation resistance in multiple genetic backgrounds, and this is dependent on the transcription factor downstream of insulin signaling, DAF-16/FOXO. Thus, this work shows that natural genetic variation in novel modifiers of insulin-signaling regulates starvation resistance.