Doctor of Philosophy (PhD)
Paternally expressed gene 3 (Peg3) is an imprinted gene encoding a DNA-binding protein that is a predicted transcriptional repressor. The two studies presented here demonstrate the repressive functions of PEG3 in regulating different cellular processes and pathways, which were observed by analyzing the ChIP-seq results systematically using both bioinformatics tools and manual inspection of significant peaks. In the first part of the work, genome-wide features of ChIP-seq peaks were characterized and the potential de novo binding motif was reevaluated. Results suggested the transcriptional repressor role of PEG3 by binding to the conserved sequence motif of the target genes. The results also revealed the unusually higher percentage of distal intergenic PEG3 peaks, suggesting the potential role of PEG3 by binding to enhancers.
Previous studies have shown that the mutant phenotypes of Peg3 are associated with the over-expression of genes involved in lipid metabolism. In addition, the initial inspection identified Acly, Fasn, Idh1, and Hmgcr as potential downstream genes. Therefore, the second part of this study was focused on assessing the functional role of PEG3 in affecting lipogenesis since these four genes are the critical genes in the lipogenesis pathway. In vivo binding of PEG3 to the promoter region of these four key genes was confirmed through individual ChIP experiments. The opposite response of Acly expression levels against the variable gene dosages of Peg3, involving 0x, 1x, and 2x Peg3 was observed. This confirmed the transcriptional repressor role of Peg3 in the expression levels of Acly. Another set of analyses showed a sex-biased response in the expression levels of Acly, Fasn, and Idh1 against 0x Peg3 with higher levels in female and lower levels in male mammary glands. These results highlighted that Peg3 may be involved in regulating the expression levels of several key genes in adipogenesis.
Overall, this study presented in this dissertation contributes to further our understanding of the regulation and functional aspects of Peg3 and other imprinted genes.
Ghimire, Subash, "Genome-Wide Analysis Of Peg3 Downstream Genes" (2021). LSU Doctoral Dissertations. 5669.