Distinguishing features of guide and substrate RNA recognition by H/ACA snoRNPs

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Kelly, Erin Katelyn
University of Lethbridge. Faculty of Arts and Science
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Lethbridge, Alta. : Universtiy of Lethbridge, Department of Chemistry and Biochemistry
H/ACA small nucleolar ribonucleoproteins (snoRNPs) pseudouridylate RNA in eukaryotes and archaea. They consist of four proteins and a guide RNA. It is unclear which element of the guide RNA the H/ACA proteins recognize. By designing guide RNA variants with altered structural features, I determined that H/ACA proteins bind guide RNA extremely tightly, but non-specifically in vitro. Additionally, the base-pairing between guide and substrate RNA varies widely in nature. To elucidate substrate selection rules, I systematically altered the sequence of a substrate RNA and tested for snoRNP binding and activity. All substrate RNA variants tested are bound by the H/ACA snoRNP, but not all are effectively modified. Minimal continuous base pairing is required to position the target uridine in the active site for modification, and H/ACA snoRNPs can target structured RNAs. This information will improve the prediction of novel target sites of H/ACA snoRNPs, e.g. in messenger RNAs.
RNA modification , H/ACA snoRNP , Saccharomyces cerevisiae , guide RNA , substrate RNA , Pseudouridine , Nucleoproteins , Non-coding RNA , Molecular biology , Dissertations, Academic