The Existence and Localization of Nuclear snoRNAs in Arabidopsis thaliana Revisited.

Deniz Streit,Enrico Schleiff,Thiruvenkadam Shanmugam,Asen Garbelyanski,Stefan Simm

doi:10.3390/plants9081016

Abstract

Ribosome biogenesis is one cell function-defining process. It depends on efficient transcription of rDNAs in the nucleolus as well as on the cytosolic synthesis of ribosomal proteins. For newly transcribed rRNA modification and ribosomal protein assembly, so-called small nucleolar RNAs (snoRNAs) and ribosome biogenesis factors (RBFs) are required. For both, an inventory was established for model systems like yeast and humans. For plants, many assignments are based on predictions. Here, RNA deep sequencing after nuclei enrichment was combined with single molecule species detection by northern blot and in vivo fluorescence in situ hybridization (FISH)-based localization studies. In addition, the occurrence and abundance of selected snoRNAs in different tissues were determined. These approaches confirm the presence of most of the database-deposited snoRNAs in cell cultures, but some of them are localized in the cytosol rather than in the nucleus. Further, for the explored snoRNA examples, differences in their abundance in different tissues were observed, suggesting a tissue-specific function of some snoRNAs. Thus, based on prediction and experimental confirmation, many plant snoRNAs can be proposed, while it cannot be excluded that some of the proposed snoRNAs perform alternative functions than are involved in rRNA modification.

Highlights

Ribosome biogenesis is a complex process with multifaceted steps involving rRNA synthesis, ribosomal protein expression and subsequent transport into the nucleus, rRNA modifications and folding, as well as protein assembly [1,2,3,4,5,6]
Ribosome biogenesis is regulated by many ribosome biogenesis factors (RBFs [1,2,3,4,5,6]) and small nucleolar RNAs, usually components of ribonucleolar particles named snoRNPs [19]
12 million reads obtained by sequencing the RNA of the total fraction as well as 7 or 15 million reads of the nuclear fractions were mapped to the genome of A. thaliana (Figure 1b)

Summary

Introduction

Ribosome biogenesis is a complex process with multifaceted steps involving rRNA synthesis, ribosomal protein expression and subsequent transport into the nucleus, rRNA modifications and folding, as well as protein assembly [1,2,3,4,5,6]. Ribosome biogenesis is regulated by many ribosome biogenesis factors (RBFs [1,2,3,4,5,6]) and small nucleolar RNAs (snoRNAs), usually components of ribonucleolar particles named snoRNPs [19]. SnoRNAs are essential small RNA molecules that have been identified to regulate and guide the posttranscriptional chemical modifications of rRNA, namely 20 O-methylation and pseudouridylation [20,21,22]. They are found in many organisms including archaea (despite the absence of a nucleolus) and eukaryotes but are notably absent in bacteria. The snoRNAs are classified according to globally conserved canonical sequence motifs known as C/D box and H/ACA boxes [20,24,25]

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Conclusion