Genetic and Epigenetic Responses to Nutrient Stress in Caenorhabditis elegans

Abstract

All organisms experience fluctuations in nutrient availability, yet our understanding of how physiology adapts to nutrient stress remains incomplete. Some response mechanisms are deeply conserved across taxa, while others have evolved in a species-specific manner to accommodate niche environmental pressures. Among the conserved mechanisms is the insulin/IGF-1 signaling (IIS) pathway, which integrates environmental cues with physiological responses to regulate development, metabolism, fitness, and ageing in response to stress. Although the canonical components of this pathway have been extensively studied, many of the downstream effectors of IIS remain elusive. The nematode Caenhorhabditis elegans is an ideal model system to study IIS in response to nutrient stress for many reasons, including its robust physiological response to starvation. C. elegans experiences boom-or-bust nutrient availability dynamics in the wild, which has driven the evolution of dramatic plastic starvation responses, such as arresting development in the first larval stage (L1 arrest) to survive extended periods of starvation. The ability to arrest development is dependent on the downstream effector of IIS, the Forkhead transcription factor DAF-16/FoxO, which engages transcriptional programs that conserve energy and support the stress response. While DAF-16 is implicated as a critical effector in many IIS-mediated stress responses, the extent to which IIS depends on DAF-16 is unclear, and the function of many downstream targets of DAF-16 are unknown. Here, we explore the epistatic relationship between insulin/IGF-1 receptor daf-2/InsR and daf-16 in early-life starvation. We use RNA-sequencing and phenotypic analysis to determine epistasis of daf-2 and daf-16 in L1 arrest and recovery. We determine that the effect of daf-2 on gene expression during L1 arrest is almost entirely daf-16-dependent, and the effects of daf-2 loss on growth following starvation is largely but not entirely daf-16-dependent. Most notably, we find that daf-2 loss preserved reproductive success following extended starvation, while daf-16 is dispensable in this context. In addition to addressing epistasis, we generate a valuable dataset for investigation of the role of IIS in mediating nutritional control of gene expression.We leverage this transcriptomic data to identify novel targets of DAF-16, including a divergent H1 histone variant hil-1, which is activated by DAF-16 during starvation. Using knock-in reporters we find that hil-1 displays highly dynamic transcriptional regulation in response to nutrient availability and IIS, with strong, ubiquitous nuclear expression during starvation. We also observe a starvation-sensitive phenotype with loss of hil-1. Using RNA-seq of hil-1 mutants, we find that hil-1 activates genes involved in the innate immune response by promoting activity of specific bZip transcription factors in the CEBP-1/NIPI-3/TRIB1 immunity pathway during starvation. Consistent with the activation of immunity genes, we find that hil-1 mutants are sensitive to bacterial pathogen exposure under reduced IIS, suggesting hil-1 connects nutrient sensing to immunity. We identify a second H1 histone variant, hil-2, which displays reciprocal transcriptional regulation to hil-1, being repressed during starvation in a DAF-16-dependent manner. We validate this dynamic regulation with knock-in reporters and predict that it promotes development when food is abundant. We find that hil-2 loss does not affect larval growth; however, our findings confirm IIS regulates H1 variants in response to nutrient status, supporting a model in which IIS alters chromatin dynamics to promote plasticity under nutrient stress. While these findings establish how IIS and DAF-16 regulate within-generation early-life starvation responses, nutrient stress in the maternal environment can also shape offspring physiology through IIS. We expand on previous work that implicates daf-2 and daf-16 as key effectors of maternal provisioning to oocytes under dietary restriction (DR) to identify downstream mechanisms that mediate soma-to-germline communication. Using tissue-specific rescue of daf-16, we identify the intestine as the primary site of action of DAF-16 for regulating embryo size in DR. We assess the effects that daf-2 and daf-16 have on embryo size and vitellogenin content, identifying a complex relationship between IIS and vitellogenin dynamics. We use RNA-seq of a daf-16 mutant and intestinal rescue of daf-16 in dietary restriction to identify intestinal targets of DAF-16 that may mediate intestine-to-germline communication under nutrient stress, which were used in a genetic screen to assess their effects on maternal provisioning.Together, this work establishes novel downstream effectors of IIS that regulate transcription and physiology in response to nutrient stress, both within and across generations. Our work expands the mechanistic framework of IIS, linking nutrient sensing, chromatin regulation, immunity, and maternal provisioning. These findings provide new insight into how conserved nutrient-sensing pathways translate environmental information into adaptive outcomes.