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

Elena Burlacu1, Fredrik Lackmann2, Lisbeth-Carolina Aguilar3, Sergey Belikov2, Rob van Nues4, Christian Trahan3,5, Ralph D. Hector6, Nicholas Dominelli-Whiteley7, Scott L. Cockroft7, Lars Wieslander2, Marlene Oeffinger3,5,8 & Sander Granneman
Nature Communications 8, Article number: 714 (2017) http://www.nature.com/articles/s41467-017-00761-8

Abstract

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.