Abstract
Subcellular compartments organize RNAs into phase-separated condensates, significantly influencing RNA metabolism. However, the study of how specific RNAs regulate interacting factors and their phenotypic outcomes is hindered by the lack of advanced imaging and regulation tools. To address this, we developed an orthogonal RNA aptamer system, Clivia-HT, which integrates a fluorescent imager with a ribonuclease-targeting chimera (RIBOTAC) degrader. This platform enables simultaneous RNA visualization and targeted degradation in living cells. Furthermore, we engineered light-activatable and light-inactivatable RIBOTACs to achieve temporal RNA degradation control. Applying this system, we demonstrated that Activating Transcription Factor 4 (ATF4) mRNA localizes to stress granules and regulates their dynamics. We also detected the role of Non-Coding RNA Activated by DNA Damage (NORAD) in RNA–protein condensate assembly. Our approach establishes a versatile method for spatiotemporal RNA manipulation, providing a powerful tool for probing RNA function in dynamic cellular environments.
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The data supporting the findings of this study are available from the corresponding authors upon request. Source data for the figures and Supplementary Figs. are provided as a Source Data file. Source data are provided with this paper.
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Acknowledgements
This work was supported by grants from the National Key R&D Program of China (2025YFC3409700 to T.D.), the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences (2025-I2M-XHXX-087 to X.L.), the National Key Research and Development Program of China (2023YFC3404102 to X.L.), the National Natural Science Foundation of China (82373784 to X.L.), and the Beijing-Tianjin-Hebei Basic Research Cooperation Special Project (J230018 to X.L.).
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J.W., K.M., and X.C. performed the experimental studies and conducted manuscript writing. H.W., H.S., Y.G., M.W., W.Z., Y.W., J.R., and M.L. carried out data analysis and manuscript validation. T.D., P.Z., and X.L. supervised the work.
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X.L., T.D., K.M., J.W., H.Y., X.C., C.A., H.S., and K.L. have filed a patent application (CN202610149905.8) related to this work. The other authors declare no competing interests.
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Wang, J., Ma, K., Cao, X. et al. An orthogonal RNA aptamer for targeted RNA regulation in phase-separated subcellular compartments. Nat Commun (2026). https://doi.org/10.1038/s41467-026-70638-2
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DOI: https://doi.org/10.1038/s41467-026-70638-2
