title: A pre-ribosomal RNA interaction network involving snoRNAs and the Rok1 helicase.
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.
authors.affiliation: Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany.
authors.forename: Roman
authors.initials: R
authors.lastname: Martin
authors.affiliation: Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany.
authors.forename: Philipp
authors.initials: P
authors.lastname: Hackert
authors.affiliation: Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt, Germany.
authors.forename: Maike
authors.initials: M
authors.lastname: Ruprecht
authors.affiliation: Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Simm
authors.affiliation: Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany.
authors.forename: Lukas
authors.initials: L
authors.lastname: Brüning
authors.affiliation: Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Mirus
authors.affiliation: Centre for Biochemistry and Molecular Cell Biology, Georg-August-University, 37073 Göttingen, Germany.
authors.forename: Katherine E
authors.initials: KE
authors.lastname: Sloan
authors.affiliation: MRC Human Genetics Unit, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Kudla
authors.affiliation: Institute for Molecular Biosciences, Goethe University, 60438 Frankfurt, Germany Cluster of Excellence Frankfurt, Goethe University, 60438 Frankfurt, Germany.
authors.forename: Enrico
authors.initials: E
authors.lastname: Schleiff
authors.affiliation: 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.
authors.forename: Markus T
authors.initials: MT
authors.lastname: Bohnsack
mesh_terms: D020029:Base Pairing; D053487:DEAD-box RNA Helicases / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012322:RNA Precursors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012337:RNA, Ribosomal, 18S / Q000235:genetics / Q000378:metabolism; D020537:RNA, Small Nucleolar / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*
chemical_list: D012322:RNA Precursors; D012335:RNA, Ribosomal; D012337:RNA, Ribosomal, 18S; D020537:RNA, Small Nucleolar; D029701:Saccharomyces cerevisiae Proteins; C120858:ROK1 protein, S cerevisiae; D053487:DEAD-box RNA Helicases
keywords: RNA helicase; RNA–protein complex; ribosome biogenesis; small nucleolar RNA