In a research article published in Science, the research teams of Prof. CHEN Lingling and LIU Jiaquan from the Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology of the Chinese Academy of Sciences reported that lncRNA SLERT is an essential RNA regulator to control the biophysical properties of the nucleolus and RNA polymerase I (Pol) I transcription via a molecular chaperone-like mechanism.
SLERT is a type of snoRNA-ended lncRNAs uncovered via non-polyadenylated RNA sequencing in human cells. SLERT is exclusively localized to the human nucleolus and enhances Pol I transcription by arranging DEAD-box RNA helicase DDX21 surrounding Pol I complexes. Of note, the human nucleolus consists of several dozens of Fibrillar centers (FCs) and dense fibrillar components (DFCs) that are essential for rDNA transcription and pre-rRNA processing, called FC/DFC units. Efficient Pol I transcription occurs on 2–3 transcriptionally active rDNAs at the FC/DFC border. Above-mentioned series were all revealed by CHEN’s team.
In the current study, the researchers revealed that DDX21 is localized largely to the periphery of FC/DFC units and that abundance of DDX21 is greatly outnumbered SLERT within each FC/DFC unit (1,000:1). Without SLERT, DDX21 exhibits hyper-multimerization to restrain nucleolar FC/DFC size and Pol I activity. DDX21 behaves fiber-like phase separation in vitro and its conformational change is closely associated with inter- or intra- multimerization and phase status. The lncRNA SLERT, even at a sub-stoichiometric ratio (from 1: 1,000 to 1:100), changes DDX21 conformation from open to closed status and results in the formation of hypo-multimerized DDX21 molecules.
In this process, SLERT prefers to bind DDX21 with open conformation, and the multimer-to-monomer transition is ever-increasing with incremental DDX21 concentration and prolonged incubation times, suggesting that SLERT promotes the DDX21 closed conformation at a sub-stoichiometric ratio though a molecular chaperone-like mechanism.
In the meanwhile, the loose DDX21 clusters surround each DFC required for proper FC/DFC liquidity and Pol I processivity in FC/DFC unit. Moreover, SLERT would inhibit DDX21’s hijacking and condensing active rDNAs for supporting Pol I efficiently occupied on rDNA to transcribe pre-rRNA.
In summary, these results reveal that SLERT acts as an RNA chaperone to promote DDX21 multimer-to-momoner transition in clusters that is required for maintaining FC/DFC units and preventing DDX21 from hijacking rDNAs.