Get in touch
If you're interested in my work or would like to collaborate, please reach out!
- awebst10@uoregon.edu
- Institute of Ecology and Evolution
University of Oregon
Eugene, OR 97401
Research
Overview
Why individuals are different from each other is one of life's fundamental puzzles. A given individual's phenotype may be driven by a combination of genetic and present environmental conditions, along with prior environmental experiences, development, or other unknown causes. The epigenetic regulation of gene expression plays an intermediate functional role between genetic or environmental perturbations and organismal phenotypes. A major goal of my research is to understand the influence of genetic and environmental variation on epigenetic and gene expression changes, and in turn, how these changes shape important traits throughout the lifespan of individuals and impact the evolution of populations. I use both experimental and theoretical approaches to address these questions. For the experimental work, I primarily use the nematode C. elegans.
Why C. elegans?
The nematode C. elegans is well-suited to support research in the area of individual variation. C. elegans primarily exist as hermaphrodites (with rare males) and do not exhibit inbreeding depression. Each individual hermaphrodite can produce roughly 300 progeny in a matter of days. In the case of inbred lines, each worm produces genetically identical progeny, making it relatively easy to generate thousands of genetically identical worms. These worms are microscopic and transparent, can be genetically altered via CRISPR or other genetic engineering approaches, and can be grown in liquid or on plates. The C. elegans genome was the first animal genome to be sequenced, and it is well annotated. In addition, the nematode community has collected and sequenced many genetically-distinct wild isolates within C. elegans as well as related nematodes in the Caenorhabditis genus from around the world. In sum, both the genetic and environmental conditions across generations can be carefully controlled with this system, and the worm community has developed resources to facilitate sophisticated analysis of the causes and consequences of variation.
Postdoctoral Research: How epigenetic differences shape fitness
Individual differences underlying reproductive traits
To gain traction on the question of why individuals are different from each other, I have honed in on part of this question: how are individuals different from each other, even when they are genetically identical? Many identical human twins exhibit divergent disease outcomes or have different traits, even when raised in similar environments, for reasons that remain poorly understood. Do micro-environmental differences or other causes lead to these differences? Genetic background cannot be controlled in humans or most other species. Using C. elegans, I am focusing on quantitative reproductive traits that are relevant to fitness, for which genetically identical individuals that develop in the same environment exhibit substantial variation. I hypothesized that gene expression differences driven by epigenetic modifications have substantial power to explain phenotypic differences across genetically identical individuals. I used single-individual transcriptomics to dissect reproductive traits, and have identified hundreds of genes for which expression variation underlies differences in these traits (many of these genes are shown in the figure to the right). Gene expression patterns of multiple genes together are highly predictive of reproductive traits, and knockdown of genes confirms causality. Genes predictive of reproductive traits are enriched for particular chromatin marks, suggesting epigenetic regulation of gene expression. You can read more about this work in our pre-print.
Heritable epigenetic variants shaping populations
Epigenetic variants that arise randomly or in response to environmental perturbations can sometimes be inherited across generations. This raises the possibility that epigenetic variation can act alongside genetic variation to shape the evolution of populations. Epigenetic variants arise more often than genetic variants, but do not typically persist for many generations (in contrast to germline DNA mutations that are faithfully inherited). I built theoretical population genetic models to understand how epigenetic variants persist long-term in populations and how they interact with genetic variants. One major result of this work is that epigenetic variants that compensate for a deleterious allele (e.g. cytosine methylation compensating for a deleterious mutation) lead to the deleterious allele being maintained at higher frequency long-term. This is shown in the figure to the right, and you can read more in our pre-print.
PhD Research: How animals endure starvation
For my dissertation research, I focused on understanding how C. elegans endure starvation. Survival in the face of limited food availability is a fitness challenge faced by virtually all organisms. C. elegans is well adapted to survive starvation conditions, as its development is coupled to food availability. When embryos hatch as L1 larvae in the absence of food, they remain developmentally arrested in the first larval stage, and this is termed L1 arrest. C. elegans larvae can survive for weeks without food during L1 arrest. Remarkably, if an arrested L1 encounters food, it recovers and the time it spent as an L1 does not count against its subsequent lifespan. It is thus considered an “ageless” state. However, we know that during L1 arrest larvae accumulate various markers of aging that are reversed upon recovery. In addition, extended time spent in L1 arrest leads to fitness consequences later in life and in subsequent generations. Further, some genes already implicated in regulating survival during L1 arrest are broadly conserved and play roles as tumor suppressors in human cancers. Given the significance of L1 arrest for understanding processes as broad as aging and intergenerational inheritance, in addition to its ecological and biomedical relevance, it is of great interest to understand how starvation resistance is regulated. To this end, I analyzed how starvation resistance is impacted by 1) transgenerational effects of ancestral starvation, 2) transcriptional regulation, and 3) genes that differ in natural populations. Each of these projects is elaborated on below.
Transgenerational effects of starvation
I found worms that experience extended dauer diapause, an environmentally-induced developmental arrest, produce great-grand progeny that exhibit increased starvation resistance as larvae and live longer as adults compared to genetically identical worms with unstarved ancestors. These worms also exhibit gene expression differences consistent with a small, genome-wide effect on the nutrient response. This effect is in contrast to the first generation following extended dauer diapause, in which worms exhibit increased inter-individual variation and decreased starvation resistance. These results suggest that ancestral environment impacts phenotypes of fitness-relevant traits several generations later. Read more about this work in our Genetics paper. A figure from this paper showing the phenotypic effects of ancestral starvation is shown to the right.
Gene-regulatory dynamics of starvation
Worms can survive L1 arrest for about two weeks, but temporal transcriptional dynamics beyond the first 24 hours and their importance for survival have not been previously characterized. I analyzed gene expression profiles of L1 larvae from immediately before hatching until death. Although worms starved different lengths of time are in the same developmental stage, mRNA transcriptional profiles continue to change even late in starvation, though the rate of gene expression change slows. Using tissue-specific and temporal depletion of RNA Pol II, we found gene expression differences occurring deep in starvation are due to a combination of reduced somatic transcription and long-term maintenance of germline transcript stability. While transcription is required in the soma early in starvation, it is (perhaps surprisingly) not required late in starvation. Germline transcriptional quiescence, already known to occur early in starvation, is maintained even deep into starvation, and this is required for reproduction upon recovery from extended starvation. You can read more about this work in our paper in Cell Reports. We were also featured on the cover, shown to the right, which shows individual gene expression trajectories for genes throughout starvation. The green and purple lines are clusters enriched for germline-expressed genes.
Natural genetic variation underlying starvation resistance
Within the C. elegans species, many genetically distinct wild isolates have been collected and whole-genome sequenced. I utilized many wild strains from this resource that represent the diversity of the species and used two high-throughput sequencing approaches to phenotype these strains for starvation resistance simultaneously. In collaboration with others, I identified strains that are particularly sensitive or resistant to starvation and uncovered regions of the genome that are important for affecting starvation resistance. The first iteration of this project using RAD-seq for phenotyping-by-sequencing has been published in G3. For the next iteration, we used MIP-seq to sequence only at sites in the genome for which each strain had a unique single-nucleotide polymorphism (SNP), thus reducing the amount of sequencing needed. We ultimately identified multiple members of the insulin receptor-like domain (irld) family containing variation (shown in the figure to the right) that affects starvation resistance and act in the insulin-like signaling pathway. You can read more about this in our paper published in eLife.
