Date of Award
Summer 6-10-2022
Degree Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
School
Biological, Environmental, and Earth Sciences
Committee Chair
Dr. Alex Sutton Flynt
Committee Chair School
Biological, Environmental, and Earth Sciences
Committee Member 2
Dr. Shahid Karim
Committee Member 2 School
Biological, Environmental, and Earth Sciences
Committee Member 3
Dr. Dmitri Mavrodi
Committee Member 3 School
Biological, Environmental, and Earth Sciences
Committee Member 4
Dr. Glenmore Shearer
Committee Member 4 School
Biological, Environmental, and Earth Sciences
Committee Member 5
Dr. Chaoyang Zhang
Committee Member 5 School
Computing Sciences and Computer Engineering
Abstract
ABSTRACT
RNA interference (RNAi) is a pervasive gene regulatory mechanism in eukaryotes based on the action of multiple classes of small RNA (sRNA). Exploiting RNAi pathways in non-model systems have great potential for creating potent RNAi technologies. Here, we accessed RNAi-mediated control of gene expression in the two-spotted spider mite, Tetranychus urticae (T. urticae) using engineered dsRNA designed to modulate the host RNAi pathway and increase RNAi efficacy. Analysis of Dicer (Dcr) generated fragments revealed how exogenous RNAs access the host RNAi pathway in this animal, opening avenues for designing RNAi technology for their control. Further, some organisms incorporate RNA-dependent RNA polymerases (RdRPs) activity into RNAi pathways either through precursor amplification or by directly generating sRNAs from Dcr-generated fragments. While this enzymatic activity has prominent roles in plants and fungi, the involvement of RdRP in RNAi pathways of many animals is controversial. In this work, we investigated the contribution of RdRP to sRNA biogenesis in Branchiostoma floridae (B. floridae), as well as their potential role in the RNAi pathways of Crassostrea gigas (C. gigas) challenged with oyster herpes virus type 1 (OsHV-1). With adequate RdRP transcripts expressed in a variety of organs and tissues and at different stages of development in these animals, their translation is highly likely. Through inhibiting RNA Pol II’s activity and analyzing potentially RdRP synthesized nascent RNAs, we detected RdRP activity restricted to a few loci. Using this approach, we implicated RdRPs in playing a critical role in somatic genome protection through transposon repression. Although we failed to recover a wide coverage of RdRP activity in Amphioxus genome. Our observation suggests a scenario where RdRP function has become marginal, consistent with their loss in several animal lineages such as vertebrates. These explain the challenges of detecting a role in the creation of dsRNA. This observation shows a framework for how an essential gene regulation mechanism slowly decays on its way to being lost.
Recommended Citation
Peter, Jacob Oche, "CHARACTERIZING ENDOGENOUS DICER PRODUCTS TO UNRAVEL NOVEL RNAI BIOGENESIS PATHWAYS" (2022). Dissertations. 2008.
https://aquila.usm.edu/dissertations/2008
Included in
Bioinformatics Commons, Biotechnology Commons, Computational Biology Commons, Evolution Commons, Genomics Commons, Immunity Commons, Laboratory and Basic Science Research Commons, Marine Biology Commons, Molecular Genetics Commons