Genetic and Environmental Mechanisms Affecting Gene Expression in Evolution and Development of Two Heliocidaris Sea Urchin Species

In this thesis, I investigate the influence of three different factors (environment, chromatin regulation, and genome structure) on gene expression in the evolution and development of the sea urchin species Heliocidaris erythrogramma and Heliocidaris tuberculata. This species pair share a recent common ancestor but exhibit different life history modes, and thus are an excellent model for studying how evolution acts over (relatively) short time scales to influence phenotype. In Chapter 1, I provide an overview of the research that has been conducted on this species pair over the past several decades. I also survey the literature on gene expression in the context of evolution and development, and discuss the various mechanisms that influence gene expression. In Chapter 2, I evaluate how gene expression in H. erythrogramma is affected by exposure to low-pH seawater, in an effort to quantify how this species may be affected by ocean acidification (OA) caused by anthropogenic climate change. It has been previously shown that OA from seawater uptake of rising carbon dioxide emissions impairs development in marine invertebrates, particularly in calcifying species. Plasticity in gene expression is thought to mediate many of these physiological effects, but how these responses change across life history stages remains unclear. The abbreviated lecithotrophic development of the sea urchin Heliocidaris erythrogramma provides a valuable opportunity to analyze gene expression responses across a wide range of life history stages, including the benthic, post-metamorphic juvenile. I measured the transcriptional response to OA in H. erythrogramma at three stages of the life cycle (embryo, larva, and juvenile) in a controlled breeding design. The results reveal a broad range of strikingly stage-specific impacts of OA on transcription, including changes in the number and identity of affected genes; the magnitude, sign, and variance of their expression response; and the developmental trajectory of expression. The impact of OA on transcription was notably modest in relation to gene expression changes during unperturbed development and dwarfed by genetic contributions from parentage. The latter result suggests that natural populations may provide an extensive genetic reservoir of resilience to OA. Taken together, these results highlight the complexity of the molecular response to OA, its substantial life history stage specificity, and the importance of contextualizing the transcriptional response to pH stress in light of normal development and standing genetic variation to better understand the capacity for marine invertebrates to adapt to OA. In Chapter 3, I examine the regulation of chromatin accessibility, and investigate how the mechanisms that govern regulatory element accessibility are similar to or different from those that govern gene expression. Chromatin accessibility plays an important role in shaping gene expression patterns across development and evolution, but little is known about the genetic and molecular mechanisms that influence chromatin configuration itself. Because cis and trans influences can both theoretically influence the accessibility of the epigenome, I sought to better characterize the role that both mechanisms play in altering chromatin accessibility in H. tuberculata and H. erythrogramma. Using hybrids of the two species, and adapting a statistical framework previously developed for the analysis of cis and trans influences on the transcriptome, I examined how these mechanisms shape the regulatory landscape at three important developmental stages, and compared my results to similar patterns in the transcriptome. I found extensive cis- and trans-based influences on evolutionary changes in chromatin, with cis effects slightly more numerous and larger in effect. Additionally, I found that genetic mechanisms influencing gene expression and chromatin configuration are correlated, but differ in several important ways. Maternal influences also appear to have more of an effect on chromatin accessibility than on gene expression, persisting well past the maternal-to-zygotic transition. Furthermore, chromatin accessibility near GRN genes appears to be regulated differently than the rest of the epigenome, and indicates that trans factors may play an outsized role in the configuration of chromatin near these genes. Together, these results represent the first attempt to quantify cis and trans influences on evolutionary divergence in chromatin configuration in an outbred natural study system, and suggest that the regulation of chromatin is more genetically complex than was previously appreciated. In Chapter 4, I consider how genomic architecture differs in H. tuberculata, H. erythrogramma, and the outgroup species L. variegatus, and how alterations in genome structure may be tied to gene expression differences between these three species. There is not a strong consensus on the connection between genome architecture and evolution, though many studies have related certain elements of genome structural variation to alterations in gene expression. Using chromosome-level genome assemblies and phylogenetic orthology inference, I found that genome-wide synteny is tied to divergence time, and that genes within syntenic regions tend to be conserved in function and copy number compared genes in non-syntenic regions. I also leveraged existing RNA-seq and ATAC-seq datasets for these species to demonstrate that genes in rearranged regions exhibit larger between-species differences in overall gene expression and altered regulatory architecture relative to genes in syntenic regions. Furthermore, in comparing my between-species comparisons of genome architecture, I was able to evaluate the extent to which genomic structural variation might underlie the gene expression differences seen in the transition to lecithotrophy. I found that “isolated” genes (individual orthologs that fall outside of syntenic blocks) exhibit particularly dramatic differences in expression trajectory within the Heliocidaris comparison; moreover, I demonstrate that the large amount of unique sequence in the H. erythrogramma genome harbors regulatory elements that alter gene expression in this species. Together, these results show that the locations of breakpoints regions in this phylogeny are unlikely to be random, and in fact have measurable influences on gene expression and, potentially, life history strategy. In Chapter 5, I contextualize the conclusions from these three studies by considering how I might add to them in the future, and also provide concluding remarks on the impact of my thesis.