RNA is required for the integrity of multiple nuclear and cytoplasmic membrane‐less RNP granules

Numerous membrane‐less organelles, composed of a combination of RNA and proteins, are observed in the nucleus and cytoplasm of eukaryotic cells. These RNP granules include stress granules (SGs), processing bodies (PBs), Cajal bodies, and nuclear speckles. An unresolved question is how frequently RNA molecules are required for the integrity of RNP granules in either the nucleus or cytosol. To address this issue, we degraded intracellular RNA in either the cytosol or the nucleus by the activation of RNase L and examined the impact of RNA loss on several RNP granules. We find the majority of RNP granules, including SGs, Cajal bodies, nuclear speckles, and the nucleolus, are altered by the degradation of their RNA components. In contrast, PBs and super‐enhancer complexes were largely not affected by RNA degradation in their respective compartments. RNA degradation overall led to the apparent dissolution of some membrane‐less organelles, whereas others reorganized into structures with altered morphology. These findings highlight a critical and widespread role of RNA in the organization of several RNP granules. Synopsis It is unclear whether RNA is required for the integrity of all the diverse types of RNP granules found in the nucleus and cytoplasm of eukaryotic cells. Here, degradation of intracellular RNA in either the cytosol or the nucleus is found to alter the majority of membrane‐less RNA protein granules, indicating a widespread RNA role in their organization. Loss of cytoplasmic RNA has a differential effect on stress granules and processing bodies, where P‐bodies are largely not altered. Targeting RNase L to the nucleus provides an inducible means to degrade nuclear RNA. Loss of nuclear RNA alters the assembly of the nucleolus, nuclear speckles, and Cajal bodies. Loss of nuclear RNA does not alter the size or number of transcriptional condensates. Graphical Abstract Targeted degradation of nuclear or cytoplasmic RNA uncovers differential roles for RNA in maintaining specific RNP granules.