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RNA. 2014 Aug;20(8):1173-82. doi: 10.1261/rna.044669.114. Epub 2014 Jun 19.

A pre-ribosomal RNA interaction network involving snoRNAs and the Rok1 helicase.

Author information

1
Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany.
2
Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt, Germany.
3
MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.
4
Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt, Germany Cluster of Excellence Frankfurt, Goethe University, 60438 Frankfurt, Germany.
5
Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany Cluster of Excellence Frankfurt, Goethe University, 60438 Frankfurt, Germany Göttingen Center for Molecular Biosciences, Georg-August-University, 37073 Göttingen, Germany.

Abstract

Ribosome biogenesis in yeast requires 75 small nucleolar RNAs (snoRNAs) and a myriad of cofactors for processing, modification, and folding of the ribosomal RNAs (rRNAs). For the 19 RNA helicases implicated in ribosome synthesis, their sites of action and molecular functions have largely remained unknown. Here, we have used UV cross-linking and analysis of cDNA (CRAC) to reveal the pre-rRNA binding sites of the RNA helicase Rok1, which is involved in early small subunit biogenesis. Several contact sites were identified in the 18S rRNA sequence, which interestingly all cluster in the "foot" region of the small ribosomal subunit. These include a major binding site in the eukaryotic expansion segment ES6, where Rok1 is required for release of the snR30 snoRNA. Rok1 directly contacts snR30 and other snoRNAs required for pre-rRNA processing. Using cross-linking, ligation and sequencing of hybrids (CLASH) we identified several novel pre-rRNA base-pairing sites for the snoRNAs snR30, snR10, U3, and U14, which cluster in the expansion segments of the 18S rRNA. Our data suggest that these snoRNAs bridge interactions between the expansion segments, thereby forming an extensive interaction network that likely promotes pre-rRNA maturation and folding in early pre-ribosomal complexes and establishes long-range rRNA interactions during ribosome synthesis.

KEYWORDS:

RNA helicase; RNA–protein complex; ribosome biogenesis; small nucleolar RNA

PMID:
24947498
PMCID:
PMC4105744
DOI:
10.1261/rna.044669.114
[Indexed for MEDLINE]
Free PMC Article

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