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Nat Commun. 2017 Sep 28;8(1):714. doi: 10.1038/s41467-017-00761-8.

High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast.

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Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, EH9 3BF, UK.
Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.
Institut de Recherches Cliniques de Montréal RNP Biochemistry laboratory, Systems Biology Axis, Montréal, QC, H2W 1R7, Canada.
Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3FF, UK.
Université de Montréal Département de Biochimie et Médecine Moléculaire Faculté de Médecine, Montréal,, QC, H3C 3J7, Canada.
Institute of Neuroscience and Psychology, University of Glasgow, Glasgow, G12 8QB, UK.
EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK.
McGill University Division of Experimental Medicine Department of medicine, Montréal, QC, H4A 3J1, Canada.
Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, EH9 3BF, UK.


While the protein composition of various yeast 60S ribosomal subunit assembly intermediates has been studied in detail, little is known about ribosomal RNA (rRNA) structural rearrangements that take place during early 60S assembly steps. Using a high-throughput RNA structure probing method, we provide nucleotide resolution insights into rRNA structural rearrangements during nucleolar 60S assembly. Our results suggest that many rRNA-folding steps, such as folding of 5.8S rRNA, occur at a very specific stage of assembly, and propose that downstream nuclear assembly events can only continue once 5.8S folding has been completed. Our maps of nucleotide flexibility enable making predictions about the establishment of protein-rRNA interactions, providing intriguing insights into the temporal order of protein-rRNA as well as long-range inter-domain rRNA interactions. These data argue that many distant domains in the rRNA can assemble simultaneously during early 60S assembly and underscore the enormous complexity of 60S synthesis.Ribosome biogenesis is a dynamic process that involves the ordered assembly of ribosomal proteins and numerous RNA structural rearrangements. Here the authors apply ChemModSeq, a high-throughput RNA structure probing method, to quantitatively measure changes in RNA flexibility during the nucleolar stages of 60S assembly in yeast.

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