DNA methylation variation in gametes and larvae of the Pacific oyster, Crassostrea gigas

Abstract

Epigenetics describes DNA modifications that change gene expression without altering the underlying nucleotide sequence. Epigenetic mechanisms such as DNA methylation can change genome function under external influences. The focus of this project is examining one epigenetic modification, DNA methylation, in oysters. DNA methylation has been well studied in vertebrates, but remains understudied in invertebrates. Furthermore, the amounts and functions of DNA methylation in organisms are extremely diverse and variable across taxa. This thesis determines patterns of DNA methylation in C. gigas to elucidate the functional role of DNA methylation. The first chapter examines the genome-wide DNA methylation profile in C. gigas male gamete cells using whole-genome bisulfite sequencing. RNA-Seq analysis was also performed on the same tissue to provide insight into the mechanisms by which DNA methylation impacts transcriptional processes. The work presented in Chapter 2 examines methylation patterns of C. gigas during early oyster developmental stages (spermatozoa and larvae). Together these data were used to test the predictions that DNA methylation is involved in gene regulatory activity and is heritable. This work also describes individual variation, parental transmission and developmental patterns of DNA methylation in oysters. Our results indicate a positive relationship between DNA methylation and gene expression, and that DNA methylation patterns are inherited in oysters.