A Genomic Exploration of Transposable Element and piRNA Occupancy, Abundance, and Functionality
Abstract
The research herein aims to promote a better understanding of the occupancy, architecture, and diversity of transposable elements and piRNA clusters across species. Transposable elements are identified, characterized, and classified in an effort to pursue molecular strategies to control a species regarded among the most significant agricultural pests, Ceratitis capitata. I present a software tool available for general use, piClusterBusteR, that is capable of quickly and accurately annotating the contents of piRNA clusters in any species of interest. The conserved architecture, yet tissue-specific
nature of piRNA clusters is described in the ovaries and testes of 13 Metazoan species. A reproducible and statistically significant metric is also demonstrated regarding the relative utilization of piRNA amplification. This software, TruePaiR, generated benchmark values for comparison and context in notable tissues and species, as well as demonstrated the capability to identify subtle differences in piRNA biogenesis across control and experimental conditions. Finally, a bioinformatic workflow is generated to observe the potential for piRNA-mediated post-transcriptional regulation via poly(A) deadenylation of protein-coding genes. By further understanding the presence, architecture, and targets of transposable elements and piRNAs, this research contributes to knowledge of the organismal evolution and development, as well as the conservation and potential to engineer the piRNA pathway in a therapeutic context across species.