In eukaryotic cells, the nucleolus is the central site for ribosome biogenesis. It is composed of distinct subcompartments: Fibrillar Center (FC), Dense Fibrillar Component (DFC), Periphery of DFC (PDFC), and Granular Component (GC), each executing specific steps in pre-rRNA transcription, processing, and ribosomal subunit assembly.
Nucleolar dysfunction is implicated in various diseases such as cancer, neurodegeneration, and developmental disorders. While the traditional view thought that rRNA synthesis and processing occur in FC-DFC units, and ribosome assembly occurs in GC, how these compartments functionally coordinate to support efficient ribosome production had remained unknown.
In a study published in Nature, the team led by Prof. CHEN Ling-Ling from the Center for Excellence in Molecular Cell Science (Shanghai Institute of Biochemistry and Cell Biology) of the Chinese Academy of Sciences uncovered a spatiotemporal separation in the processing of distinct ribosomal RNA precursors (pre-rRNAs) within the nucleolus, offering a new perspective on how nucleolar architecture is functionally organized.
By integrating metabolic labeling, single-molecule RNA imaging, super-resolution microscopy, and quantitative proteomics, this study systematically mapped the spatiotemporal distribution of pre-rRNA processing in the nucleolus. It uncovered that small subunit (SSU) pre-rRNA is predominantly processed within the inner FC–PDFC regions and largely completes its processing within the first 30 minutes. While the large subunit (LSU) pre-rRNA is enriched in the outer PDFC–GC regions and matures gradually after 30 minutes. This spatial separation contradicts traditional models that placed both processing steps within the GC, and redefines our understanding of specialized functions within nucleolar subdomains.
Such a compartmentalized processing is functionally significant. In slow-proliferation or differentiated cells, nucleoli exhibit fewer but enlarged FC-DFC units, accompanying with less efficient SSU processing, and accumulated SSU pre-rRNAs near the inner nucleolar regions, ultimately resulting in reduced production of ribosomes.
To quantify the relationship, researchers introduced the new geometric parameter, named Relative FC/DFC interface, which quantitatively links individual nested FC/DFC structures with the SSU processing efficiency. Furthermore, antisense oligonucleotides (ASOs) targeting the 5′ ETS region of SSU pre-rRNA were used to inhibit pre-rRNA processing, recapitulating the structural defects observed in slow-proliferation cells. These results collectively revealed an essential role of 5' ETS-centered SSU processing in maintaining nucleolar substructures.
Notably, evolutionary comparisons further supported the model. Bipartite nucleoli in anamniotes such as zebrafish, which lack a separated FC–DFC interface, exhibited distinct 5′ ETS distribution and much slower pre-rRNA diffusion compared to multilayered nucleoli in amniotes. Introducing an artificial FC/DFC interface to bipartite nucleoli led to enhanced processing efficiency, suggesting that the emergence of multilayered nucleolar organization may have conferred evolutionary advantages in ribosome production.
Together, this study has established a direct link between molecular-level function and micron-level nucleolar architecture, revealing the dynamic coordination between pre-rRNA processing and nucleolar substructure, and offering potential strategies for nucleolus-related disease treatment via targeting key steps of ribosome biogenesis within nucleolar substructures.
Reference: https://www.nature.com/articles/s41586-025-09412-1
Appendix：
