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- All Subjects: microRNA
- Creators: Herrera-Quiroz, Demian David
I hypothesize that duplication events grant miRNA families with enhanced regulatory capabilities, specifically through distinct targeting preferences by family members. This has relevance for our understanding of vertebrate evolution, as well disease detection and personalized medicine. To test this hypothesis, I apply a conjunction of bioinformatic and experimental approaches, and design a novel high-throughput screening platform to identify human miRNA targets. Combined with conventional approaches, this tool allows systematic testing for functional targets of human miRNAs, and the identification of novel target genes on an unprecedented scale.
In this dissertation, I explore evolutionary signatures of 62 deeply conserved metazoan miRNA families, as well as the targeting preferences for several human miRNAs. I find that constraints on miRNA processing impact sequence evolution, creating evolutionary hotspots within families that guide distinct target preferences. I apply our novel screening platform to two cancer-relevant miRNAs, and identify hundreds of previously undescribed targets. I also analyze critical features of functional miRNA target sites, finding that each miRNA recognizes surprisingly distinct features of targets. To further explore the functional distinction between family members, I analyze miRNA expression patterns in multiple contexts, including mouse embryogenesis, RNA-seq data from human tissues, and cancer cell lines. Together, my results inform a model that describes the evolution of metazoan miRNAs, and suggests that highly similar miRNA family members possess distinct functions. These findings broaden our understanding of miRNA function in vertebrate evolution and development, and how their misexpression contributes to human disease.
Medicolegal forensic entomology is the study of insects to aid with legal investigations (Gemmellaro, 2017). Insect evidence can be used to provide information such as the post-mortem interval (PMI). Blow flies are especially useful as these insects are primary colonizers, quickly arriving at a corpse (Malainey & Anderson, 2020). The age of blow flies found at a scene is used to calculate the PMI. Blow fly age can be estimated using weather data as these insects are poikilothermic (Okpara, 2018). Morphological analysis also can be used to estimate age; however, it is more difficult with pupal samples as the pupae exterior does not change significantly as development progresses (Bala & Sharma, 2016). Gene regulation analysis can estimate the age of samples. MicroRNAs are short noncoding RNA that regulate gene expression (Cannell et al., 2008). Here, we aim to catalog miRNAs expressed during the development of three forensically relevant blow fly species preserved in several storage conditions. Results demonstrated that various miRNA sequences were differentially expressed across pupation. Expression of miR92b increased during mid pupation, aga-miR-92b expression increased during early pupation, and bantam, miR957, and dana-bantam-RA expression increased during late pupation. These results suggest that microRNA can be used to estimate the age of pupal samples as miRNA expression changes throughout pupation. Future work could develop a statistical model to accurately determine age using miRNA expression patterns.