Imprinted genes have been extensively documented in eutherian mammals and exhibit significant interspecific variation, both in the suites of genes that are imprinted and in their regulation between tissues and developmental stages. Much less is known about imprinted loci in metatherian (marsupial) mammals, wherein studies have been limited to a small number of genes imprinted in eutherians. In this dissertation, I used ChIP-seq and RNA-seq approaches to conduct the first ab initio search for imprinted autosomal genes in fibroblasts, fetal brain, and placenta of a metatherian mammal, the gray short-tailed opossum, Monodelphis domestica, and the first chromosome-wide study of paternally imprinted metatherian X chromosome inactivation.
Evidence from a few genes in diverse species suggests that metatherian X- chromosome inactivation is characterized by exclusive, but incomplete (leaky), repression of genes on the paternally derived X chromosome. Herein I show that the majority of opossum X-linked genes exhibit paternally imprinted expression with 100% maternal-allele expression, whereas ~14% of genes escape inactivation, exhibiting varying levels of biallelic expression. In addition, I have shown that transcriptionally opposing histone modifications correlate strongly with opossum XCI. However, the opossum did not show an association between X-linked gene expression and promoter DNA methylation. In generating the first genome-wide profile of histone modification states for a metatherian mammal, and coupling it with in-depth gene expression analyses, I identified the first set of genes imprinted in a metatherian that are not imprinted in eutherian mammals and described transcriptionally opposing histone modifications and differential DNA methylation at the promoters of a subset of these genes. My findings suggest that metatherians use multiple epigenetic mechanisms to mark imprinted genes and support the concept that lineage-specific selective forces can produce sets of imprinted genes that differ between metatherian and eutherian lines. Overall, these studies furnish a comprehensive catalog of parent-of-origin expression status for both autosomal and X-linked genes in a metatherian, Monodelphis domestica, and open new avenues for illuminating the mechanisms and evolution of imprinted gene regulation in mammals generally.
- Samollow, Paul Professor