Intellectual Merit: Every cell in an organism carries the same sets of genes. However different cells perform different functions because only subsets of genes are activated in each cell. One way that cells activate specific sets of genes is by chemically modifying particular pieces of DNA. This project investigates how one such modification, DNA methylation, affects development in the honeybee. Honeybees are well-known social insects and represent important species for studying DNA methylation because of their ecological and economic importance. In addition, the differentiation of honeybee castes represents one of the most spectacular examples of developmental plasticity: queens and workers arise from the same genes through differential gene activation mediated by DNA methylation. Consequently, determining how DNA methylation affects development in honeybees would help link specific molecular mechanisms to the production of different developmental forms and provide insight into the factors affecting social behavior.
Broader Impacts: This project will result in several broader impacts to society. For example, undergraduate and graduate students will be trained in integrative multidisciplinary research. Research findings will also be implemented in university classes and laboratories. Moreover, research findings will be disseminated through popular press and scientific meetings thereby increasing scientific literacy. Finally, because honeybees are critical species for pollinating crops, these studies will contribute to improving agricultural outcomes in the United States.
Epigenetic inheritance, defined as heritable alteration of the packaging of chromatins, is crucial to a wide array of biological processes. The focus of this project was DNA methylation, which is one of the most phylogenetically widespread, important epigenetic marks. Previous research products, including those from the PIs, indicated that DNA methylation might play an important role in determining phenotypic plasticity in insects. Specifically, DNA methylation is implicated in one of the most dramatic examples of phenotypic plasticity – namely, caste differentiation in eusocial bees. From highly similar genotypes, queens and workers emerge, each encoding extremely different and specialized phenotypes. It was proposed that epigenetic mechanisms such as DNA methylation could affect how different gene products are generated from the same genetic repertoire, determining the ultimate fate of the specific cellular development. However, we have little understanding of several basic, related questions, including: how widespread is the epigenetic inheritance in insects, how are they related to the evolution of eusociality, and how do they interact with cellular molecular machineries. This project investigated several key questions to resolve these fundamental problems. As an integral part of this project, we have examined detailed patterns of DNA methylation from several insects as well as from an outgroup of insects. These analyses showed that DNA methylation is in fact quite widespread in insects, and probably so in other invertebrates. Consequently, DNA methylation is not confined to eusocial insect species only. In fact, we showed that DNA methylation at the gene level is extremely conserved across very long evolutionary timescales. Moreover, we were able to show that different types of epigenetic modifications (such as DNA methylation and histone modifications) are also strongly correlated across long evolutionary timescales. On the other hand, our investigation also revealed that some details of DNA methylation vary between different species. Specifically, in some species, exons are more highly methylated than introns, and specific regions of the genes are more highly methylated than other regions in different species. These observations show that even though DNA methylation is conserved in general, smaller-scale modifications may occur frequently, and they may encode species-specific functional roles. The other critical aspect of this project was to understand how DNA methylation and gene expression are causatively related. Our investigation showed that the impact of DNA methylation on gene expression is quite different from the observed relationship in mammalian promoters. Unlike mammalian examples, DNA methylation in insects is mostly regulated at the body of genes rather than promoter regions. In addition, high levels of DNA methylation at the body of genes were correlated with high levels of gene expression, which is the opposite of what is observed in mammalian promoters. Therefore, our study highlights the importance of target regions of DNA methylation in its functional specificity. Moreover, we have shown that DNA methylation of some genes are highly differentiated in different castes and sexes, as well as between individuals differentially affected by specific pathogens. In addition to completing several research objectives associated with understanding DNA methylation in insects, this project also allowed the training of several scientists. Due to the interdisciplinary nature of this project, this project provided excellent synergistic training to students with very different backgrounds, from entomology to molecular biology and computational sciences. The topics investigated in this project were heavily incorporated into the undergraduate and graduate classes offered by the PI. For example the impact of DNA methylation on the determination of queen and worker bees helped students to understand the importance of epigenetically determined cell fates and phenotypic plasticity. Moreover, several peer-reviewed articles have been published as a result of this project, and discussed in the scientific community. Some of the results from the research objectives may have significant bearing to beekeeping. In addition, the PI utilizes the topics of this project in career seminars and mentoring as a part of her outreach efforts to K-12 education.
