Nucleolar Proteomics Revealed the Regulation of RNA Exosome Localization by MTR4

The nucleolus is the largest membrane-less organelle within the nucleus and plays critical roles in regulating the cell cycle, senescence, and stress responses. The RNA exosome is a multiprotein ribonucleolytic complex involved in RNA processing and degradation in the cytoplasm, the nucleus, and the nucleolus. Previous studies have shown that the subcellular localization of the RNA exosome is crucial for its function. However, the mechanism that regulates its spatial distribution remains largely unexplored. In this study, we identified the nuclear RNA helicase MTR4 as a regulator of the RNA exosome localization through nucleolar quantitative proteomics technology. Immunostaining and fluorescence tagging confirmed that the depletion of MTR4 resulted in the translocation of the RNA exosome subunits from the nucleolus to the nucleoplasm. Notably, the translocation is specifically regulated by MTR4 and does not depend on other cofactors of the MTR4-containing Trf4/5-Air1/2-Mtr4 polyadenylation, poly(A) exosome-targeting, and nuclear exosome targeting complexes. The nucleolar accumulation of exosome subunits mutually depends on other exosome subunits. Additionally, actinomycin D treatment, which inhibits transcription, induced the RNA exosome to translocate from the nucleolus to the nucleoplasm, likely through the regulation of nucleolar MTR4 levels. These findings uncover a regulatory mechanism that modulates the localization of the RNA exosome within the nucleolus.