Biology subjects

Webster, A. K.

Publications and source records attributed to Webster, A. K..

11 recordsLinked to original sources

bioRxiv2026

Large-scale pooled selection enables mapping of modifiers of RNAi gene knockdown effects in C. elegans

Genetic interactions contribute to phenotypic variation, yet most studies characterize them in a small number of reference backgrounds rather than across natural populations. Studying genetic interactions in Caenorhabditis elegans is facilitated by RNAi by feeding, which enables gene-specific knockdowns across many genetic backgrounds without the need to construct individual mutant lines. However, individually screening hundreds of isolates across many RNAi conditions is laborious. Here, we developed a pooled platform that uses whole-genome sequencing to quantify the fitness of hundreds of genetically distinct C. elegans strains competing in a single flask. We leveraged this platform to evaluate RNAi responses in a pooled population of RNAi-sensitive C. elegans strains and identified two classes of QTL that influence RNAi responses. The first class influences responses to knockdowns of specific genes and is exemplified by a QTL that is specific to knockdown of mig-6. The second class influences general RNAi-response across multiple knockdowns. One QTL in this class localized to the right arm of chromosome III and was detected by both GWA and xQTL mapping, which suggests that a common large-effect variant underlies this QTL. We identified a T96K missense change in the dsRNA receptor SID-2 as the underlying causal variant. The 96K allele resides in the extracellular domain of SID-2 and confers increased RNAi sensitivity relative to the 96T allele. We hypothesize that the 96K allele enables greater uptake of ingested lumenal dsRNA through higher-affinity binding to the dsRNA phosphate backbone. The platform we developed enables systematic mapping of genetic interactions across natural populations at a previously impractical scale.

genetics↗

bioRxiv2023

Epigenetic context predicts gene expression variation and reproductive traits across genetically identical individuals

In recent decades, genome-wide association studies (GWAS) have been the major approach to understand the biological basis of individual differences in traits and diseases. However, GWAS approaches have limited predictive power to explain individual differences, particularly for complex traits and diseases in which environmental factors play a substantial role in their etiology. Indeed, individual differences persist even in genetically identical individuals, although fully separating genetic and environmental causation is difficult in most organisms. To understand the basis of individual differences in the absence of genetic differences, we measured two quantitative reproductive traits in 180 genetically identical young adult Caenorhabditis elegans roundworms in a shared environment and performed single-individual transcriptomics on each worm. We identified hundreds of genes for which expression variation was strongly associated with reproductive traits, some of which depended on individuals historical environments and some of which was random. Multiple small sets of genes together were highly predictive of reproductive traits, explaining on average over half and over a quarter of variation in the two traits. We manipulated mRNA levels of predictive genes to identify a set of causal genes, demonstrating the utility of this approach for both prediction and understanding underlying biology. Finally, we found that the chromatin environment of predictive genes was enriched for H3K27 trimethylation, suggesting that gene expression variation may be driven in part by chromatin structure. Together, this work shows that individual, non-genetic differences in gene expression are both highly predictive and causal in shaping reproductive traits.

genomics↗

bioRxiv2022

Heritable epigenetic variation facilitates long-term maintenance of epigenetic and genetic variation

The maintenance of genetic and phenotypic variation has long been one of the fundamental questions in population and quantitative genetics. A variety of factors have been implicated to explain the maintenance of genetic variation in some contexts (e.g. balancing selection), but the potential role of epigenetic regulation to influence population dynamics has been understudied. It is well recognized that epigenetic regulation, including histone methylation, small RNA expression, and DNA methylation, helps to define differences between cell types and facilitate phenotypic plasticity. In recent years, empirical studies have shown the potential for epigenetic regulation to also be heritable for at least a few generations without selection, raising the possibility that differences in epigenetic regulation can act alongside genetic variation to shape evolutionary trajectories. Like genetic mutation, heritable differences in epigenetic regulation can arise spontaneously; these are termed epimutations. Epimutations differ from genetic mutations in two key ways - they occur at a higher rate and the loci at which they occur often revert back to their original state within a few generations. Here, we present an extension of the standard population-genetic model with selection to incorporate epigenetic variation arising via epimutation. Our model assumes a diploid, sexually reproducing population with random mating. In addition to spontaneous genetic mutation, we included parameters for spontaneous epimutation and back-epimutation, allowing for four potential epialleles at a single locus (two genetic alleles, each with two epigenetic states), each of which affect fitness. We then analyzed the conditions under which stable epialleles were maintained. Our results show that highly reversible epialleles can be maintained in long-term equilibrium under neutral conditions in a manner that depends on the epimutation and back-epimutation rates, which we term epimutation-back-epimutation equilibrium. On the other hand, epialleles that compensate for deleterious mutations cause deviations from the expectations of mutation-selection balance by a simple factor that depends on the epimutation and back-epimutation rate. We also numerically analyze several sets of fitness parameters for which large deviations from mutation-selection balance occur. Together, these results demonstrate that transient epigenetic regulation may be an important factor in the maintenance of both epigenetic and genetic variation in populations.

evolutionary biology↗

bioRxiv2021

Natural variation in the irld gene family affects insulin/IGF signaling and starvation resistance

Starvation resistance is important to disease and fitness, but the genetic basis of its natural variation is unknown. We developed a synthetic-population (re)sequencing approach using molecular inversion probes (MIP-seq) to measure relative fitness during and after larval starvation in C. elegans. We applied this competitive assay to 100 genetically diverse, sequenced, wild strains, revealing natural variation in starvation resistance. We confirmed that the most starvation-resistant strains survive and recover from starvation better than the most starvation-sensitive strain, MY2147, using standard assays. We performed genome-wide association with the MIP-seq trait data and identified three quantitative trait loci (QTL) for starvation resistance. These QTL contain several members of the Insulin/EGF Receptor-L Domain (irld) family with sequence variation associated with variation in starvation resistance. We used genome editing to show that individual modification of four irld genes increases starvation resistance of MY2147. Modification of irld-39 and irld-52 together increases starvation resistance of the laboratory-reference strain N2. Increased starvation resistance of the irld-39; irld-52 double mutant depends on daf-16/FoxO, and these worms also show increased nuclear localization of DAF-16 during starvation. DAF-16/FoxO is a widely conserved transcriptional effector of insulin/IGF signaling (IIS), and these results suggest that IRLD proteins modify IIS. This work demonstrates efficacy of using MIP-seq to dissect a complex trait, identifies irld genes as natural modifiers of starvation resistance in C. elegans, and suggests that an expanded gene family affects a deeply conserved signaling pathway to alter a fitness-proximal trait.

genetics↗

bioRxiv2021

Alternative somatic and germline gene-regulatory strategies during starvation-induced developmental arrest

Nutrient availability governs growth and quiescence, and many animals arrest development when starved. Somatic and germline cells have distinct functions and constraints, suggesting different regulatory mechanisms contribute to an integrated starvation response. Using C. elegans L1 arrest as a model, we show that gene expression changes deep into starvation. Surprisingly, relative expression of germline-enriched genes increases for days. We conditionally degraded the large subunit of RNA Polymerase II and found that early but not late somatic transcription is required for survival and that germline transcription does not affect survival. Expression analysis revealed that thousands of genes are continuously transcribed in the soma, though their absolute abundance declines, while the germ line is transcriptionally quiescent with extreme transcript stability. This work reveals alternative somatic and germline gene-regulatory strategies during starvation, with the soma relying on a robust transcriptional response to support immediate survival while the germ line relies on transcriptional quiescence and mRNA stability to maintain future reproductive success.

genetics↗

bioRxiv2020

DAF-18/PTEN inhibits germline zygotic gene activation during primordial germ cell quiescence

Quiescence, an actively-maintained reversible state of cell cycle arrest, is not well understood. PTEN is one of the most frequently lost tumor suppressors in human cancers and regulates quiescence of stem cells and cancer cells. In C. elegans mutant for daf-18, the sole C. elegans PTEN ortholog, primordial germ cells (PGCs) divide inappropriately in starvation conditions, in a TOR-dependent manner. Here, we further investigated the role of daf-18 in maintaining PGC quiescence. We found that maternal or zygotic daf-18 is sufficient to maintain cell cycle quiescence, that daf-18 acts in the germ line and soma, and that daf-18 affects timing of PGC divisions in fed animals. Importantly, our results also implicate daf-18 in zygotic germline gene activation, though not in germline fate specification. However, TOR is less important to zygotic germline gene expression, suggesting that in the absence of food daf-18/PTEN prevents inappropriate germline zygotic gene activation and cell division by distinct mechanisms.

developmental biology↗

bioRxiv2020

Balancing selection maintains ancient genetic diversity in C. elegans

Across diverse taxa, selfing species have evolved independently from outcrossing species thousands of times. The transition from outcrossing to selfing significantly decreases the effective population size, effective recombination rate, and heterozygosity within a species. These changes lead to a reduction in genetic diversity, and therefore adaptive potential, by intensifying the effects of random genetic drift and linked selection. Within the nematode genus Caenorhabditis, selfing has evolved at least three times and all three species, including in the model organism Caenorhabditis elegans, show substantially reduced genetic diversity relative to outcrossing species. Selfing and outcrossing Caenorhabditis species are often found in the same niches, but we still do not know how selfing species with limited genetic diversity can adapt to these environments. Here, we examine the whole-genome sequences from 609 wild C. elegans strains isolated worldwide and show that genetic variation is concentrated in punctuated hyper-divergent regions that cover 20% of the C. elegans reference genome. These regions are enriched in environmental response genes that mediate sensory perception, pathogen response, and xenobiotic stress response. Population genomic evidence suggests that genetic diversity in these regions has been maintained by long-term balancing selection. Using long-read genome assemblies for 15 wild strains, we show that hyper-divergent haplotypes contain unique sets of genes and show levels of divergence comparable to levels found between Caenorhabditis species that diverged millions of years ago. These results provide an example for how species can avoid the evolutionary "dead end" associated with selfing.

evolutionary biology↗

bioRxiv2019

Population selection and sequencing of C. elegans wild isolates identifies a region on chromosome III affecting starvation resistance

To understand the genetic basis of complex traits, it is important to be able to efficiently phenotype many genetically distinct individuals. In the nematode Caenorhabditis elegans, individuals have been isolated from diverse populations around the globe and whole-genome sequenced. As a result, hundreds of wild strains with known genome sequences can be used for genome-wide association studies (GWAS). However, phenotypic analysis of these strains can be laborious, particularly for quantitative traits requiring multiple measurements per strain. Starvation resistance is likely a fitness-proximal trait for nematodes, and it is related to metabolic disease risk in humans. However, natural variation in C. elegans starvation resistance has not been characterized, and precise measurement of the trait is time-intensive. Here, we developed a population selection and sequencing-based approach to phenotype starvation resistance in a pool of 96 wild strains. We used restriction site-associated DNA sequencing (RAD-seq) to infer the frequency of each strain among survivors in a mixed culture over time during starvation. We used manual starvation survival assays to validate the trait data, confirming that strains that increased in frequency over time are starvation-resistant relative to strains that decreased in frequency. These results document natural variation in starvation resistance. Further, we found that variation in starvation resistance is significantly associated with variation at a region on chromosome III. Using a near-isogenic line (NIL), we showed the importance of this genomic interval for starvation resistance. This study demonstrates the feasibility of using population selection and sequencing in an animal model for phenotypic analyses of quantitative traits, reveals natural variation of starvation resistance in C. elegans, and identifies a genomic region that contributes to such variation.

genetics↗

bioRxiv2018

Dauer diapause has transgenerational effects on starvation survival and gene expression plasticity

Phenotypic plasticity is facilitated by epigenetic regulation, and remnants of such regulation may persist after plasticity-inducing cues are gone. However, the relationship between plasticity and transgenerational epigenetic memory is not understood. Dauer diapause in Caenorhabditis elegans provides an opportunity to determine how a plastic response to the early-life environment affects traits later in life and in subsequent generations. We report that after extended diapause, post-dauer worms initially exhibit reduced reproductive success and greater inter-individual variation. In contrast, F3 progeny of post-dauers 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. Further, post-dauer F3 progeny exhibit reduced gene expression plasticity, suggesting a trade-off between plasticity and epigenetic memory. This work reveals complex effects of nutrient stress over different time scales in an animal that evolved to thrive in feast and famine.

evolutionary biology↗

bioRxiv2018

Intergenerational effects of dietary restriction on insulin/IGF signaling and reproductive development

The roundworm C. elegans transiently arrests larval development to survive extended starvation (1), but such early-life starvation reduces reproductive success (2, 3). Maternal dietary restriction (DR) buffers progeny from starvation, increasing reproductive success (4). It is unknown why early-life starvation decreases reproductive success and how maternal diet modifies this process. We show here that extended starvation in first-stage (L1) larvae followed by unrestricted feeding results in a variety of abnormalities in the reproductive system, including glp-1/Notch-sensitive germ-cell tumors and uterine masses that express neuronal and epidermal markers. We found that maternal DR reduces the penetrance of starvation-induced abnormalities, including tumors. Furthermore, we show that maternal DR reduces insulin/IGF signaling (IIS) in progeny, and that daf-16/FoxO and skn-1/Nrf, transcriptional effectors of IIS, are required in progeny for maternal DR to suppress abnormalities. daf-16/FoxO activity in somatic tissues is sufficient to suppress starvation-induced abnormalities, suggesting cell-nonautonomous regulation of reproductive system development. This work reveals complex inter- and intra-generational effects of nutrient availability mediated by IIS with consequences on developmental integrity and reproductive success.\n\nOne Sentence SummaryIntergenerational effects of diet on IIS

developmental biology↗

bioRxiv2018

Perception of environmental polypeptides in C. elegans activates insulin/IGF signaling and alters lipid metabolism

Food perception affects animal physiology in complex ways. We uncoupled the effects of food perception and ingestion in the roundworm C. elegans. Perception was not sufficient to promote development, but larvae exposed to food without ingestion failed to develop upon return to normal culture conditions. Inhibition of gene expression during perception rescued subsequent development, demonstrating the response to perception without feeding is deleterious. Perception altered DAF-16/FOXO localization, reflecting activation of insulin/IGF signaling (IIS). The insulin-like peptide daf-28 was specifically required, suggesting perception in chemosensory neurons directly regulates peptide secretion. Gene expression and Nile Red staining suggest that perception alters lipid metabolism. Environmental polypeptides are sensed by starved larvae and promote dauer diapause recovery. We conclude that polypeptides are perceived as a food-associated cue, initiating a signaling and gene regulatory cascade that alters metabolism in anticipation of feeding and development, but that this response is detrimental if feeding does not occur.

developmental biology↗