Date of Award
8-23-2024
Degree Type
Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Biology
Advisor(s)
Eleanor Maine
Keywords
3' tailing;C. elegans;development;poly(U) polymerase;RNA;uridylation
Subject Categories
Biology | Life Sciences
Abstract
A continuously growing body of work has shown that RNA regulation is an essential aspect of germline development across metazoans. However, another layer of regulation exists “above” this: post-transcriptional modifications to RNAs can alter their function and affect biological activity. Poly(U) polymerases (PUPs) add uridines to the 3’ end of RNA molecules, a process called uridylation, or U-tailing. Previous research has identified the importance of PUPs in C. elegans development, and this work here aims to elucidate the function of PUPs at the molecular level. Using pup-1, pup-2, pup-3, and pup-4 deletion mutants in small RNA-seq, long-read mRNA-seq, and short-read mRNA-seq experiments, we examined changes in small RNA and mRNA uridylation and abundance. Our results show that the PUP enzymes have differential activity on both RNA target types and at different developmental stages. We found that PUP-1 is primarily responsible for U-tailing siRNAs and that PUP-4 limits uridylation activity on small RNAs. PUP-3 is primarily responsible for the addition of U-tails on non-adenylated mRNAs. Uridylation on small RNAs or mRNAs is not eliminated in a quadruple pup mutant, suggesting that another enzyme can add U-tails in the absence of PUPs. In adults, PUP-1 modulates the abundance of hundreds of mRNAs, while in embryos, PUP-2 is the dominant modulator. However, PUP-1 is essential in the clearance of ectopic PGL granules in the early embryo and defects in the timing of division of the founder germ cell are associated with reduced fecundity as adults. Ultimately, this in-depth analysis of uridylation in pup deletion mutants has enhanced our understanding of uridylation’s role in germline regulation and how this tailing modification fits into RNA regulation pathways in general.
Access
Open Access
Recommended Citation
Kelley, Leanne Helen, "Poly(U) polymerases have complex roles in modulating the small RNAome and transcriptome of C. elegans" (2024). Dissertations - ALL. 1982.
https://surface.syr.edu/etd/1982
