Specialized box C/D snoRNPs act as antisense guides to target RNA base acetylation.

Sunny Sharma,Karl-Dieter Entian,Peter Kötter,Denis L J Lafontaine,Rob Van Nues,Jun Yang,Peter Watzinger,Sander Granneman,Mihaela Zavolan

doi:10.1371/journal.pgen.1006804

Abstract

Box C/D snoRNAs are known to guide site-specific ribose methylation of ribosomal RNA. Here, we demonstrate a novel and unexpected role for box C/D snoRNAs in guiding 18S rRNA acetylation in yeast. Our results demonstrate, for the first time, that the acetylation of two cytosine residues in 18S rRNA catalyzed by Kre33 is guided by two orphan box C/D snoRNAs–snR4 and snR45 –not known to be involved in methylation in yeast. We identified Kre33 binding sites on these snoRNAs as well as on the 18S rRNA, and demonstrate that both snR4 and snR45 establish extended bipartite complementarity around the cytosines targeted for acetylation, similar to pseudouridylation pocket formation by the H/ACA snoRNPs. We show that base pairing between these snoRNAs and 18S rRNA requires the putative helicase activity of Kre33, which is also needed to aid early pre-rRNA processing. Compared to yeast, the number of orphan box C/D snoRNAs in higher eukaryotes is much larger and we hypothesize that several of these may be involved in base-modifications.

Highlights

Non-coding RNA represents the most abundant form of gene expression in eukaryotic cells [1]
Some box C/D snoRNAs, like yeast U3, U14 and U8 in higher eukaryotes are not involved in methylation but are essential for pre-rRNA processing
Biochemical and computational analyses have led to the identification and characterization of most box C/D snoRNA targets

Summary

Introduction

Non-coding RNA (ncRNA) represents the most abundant form of gene expression in eukaryotic cells [1]. Box C/D snoRNPs catalyze sitedirected 20-O-ribose methylation, whereas H/ACA snoRNPs catalyze site-directed pseudouridylations of specific rRNA nucleotides [2]. RNAse MRP and some box C/D snoRNAs, like U3, U14 and U8 in higher eukaryotes are involved in pre-rRNA processing. The RNA component of box C/D and box H/ACA snoRNPs functions as an adaptor to guide the catalytic activity of the modification enzyme associated with the RNP to its target site [1]

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Discussion

Conclusion