Browsing by Subject "genome assembly"

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    CBD and CpGs: Cannabidiol Neuroepigenetics and a Novel Allele-Specific DNA Methylation Pipeline
    (2023-05) Flack, Nicole
    DNA methylation is an epigenetic mechanism that connects lifestyle and environment to the largely static nucleotide sequence of the genome, influencing function across individual, generational, and evolutionary timescales. Advances in sequencing technology have greatly expanded epigenetic data availability; however, significant technical limitations and knowledge gaps remain. The research presented here interrogates genome-wide differential DNA methylation in three contexts: direct adult cannabidiol (CBD) exposure, developmental CBD exposure, and de novo genome assembly for a non-model species. The objective of the first study was to assess the neuroepigenetic activity, if any, of a popular non-intoxicating phytocannabinoid during direct exposure in adult mice. This work represents the first published exploration of CBD's influence on the brain epigenome; functional analysis of differentially methylated genes revealed changes putatively associated with psychiatric phenotypes. The second study evaluated the consequences of developmental CBD exposure on the adult mouse brain epigenome and behavior. This work revealed persistent, sex-specific behavior changes and perturbed brain DNA methylation in the exposed adult offspring. The third study applied standalone nanopore sequencing for de novo}genome assembly and allele-specific DNA methylation analysis of Pallas's cat (Otocolobus manul), and generated one of the highest-quality reference genomes currently available in Felidae. In the future, this pipeline can be applied to environmental epigenetics experiments to simultaneously obtain genomic and epigenomic data while circumventing several pitfalls of short-read DNA methylation analysis. Collectively, my results illustrate the value of DNA methylation analysis for investigating the functional consequences of a novel exposure, and provide resources for future work in the area of comparative genomics and epigenomics.