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bioRxiv · 10.64898/2026.07.15.738841

Multidimensional atlas of RNA-regulated proteins revealed by RNA-dependent thermal proteome profiling

Chen, Y.·Liu, Z.·Wang, Y.·Lu, W.·Li, H.·Wang, W.·Qiu, Z.·Qiu, Y.·Qing, H.·Xie, Y.·Liu, N.·Zhang, C.·Qin, W.
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Abstract

RNA and proteins interact pervasively in cellular processes, yet the functional relevance of most RNA-binding proteins remains unknown. To address this, we developed RNA-dependent thermal proteome profiling (RTPP), a method that identifies RNA-regulated proteins (RRPs) by detecting changes in a proteins structural stability upon RNA binding, without requiring crosslinking or enrichment. Applying RTPP in HEK293T cells revealed 1,664 RRPs, including 257 previously undetected RNA-binding "orphans". One such orphan, SGK3, binds the lncRNA CASC15, facilitating its PtdIns(3)P binding, endosomal recruitment and kinase activity. We further generated a tissue-specific RRP atlas, identifying interactions unique to particular organs, including hippocampus-specific RRPs dysregulated in Alzheimers disease. Integrating RTPP with proximity labeling resolved RNA-binding heterogeneities across subcellular compartments. Live-cell RNase treatment also uncovered proteins associated with cell surface RNA, revealing that RO60 form nanoscale clusters with glycoRNA. RTPP provides a powerful approach to decipher functional RNA-protein interactions across multiple biological dimensions.

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Chen, Y., Liu, Z., Wang, Y., Lu, W., Li, H., Wang, W., Qiu, Z., Qiu, Y., Qing, H., Xie, Y., Liu, N., Zhang, C., Qin, W.. 2026-07-16. Multidimensional atlas of RNA-regulated proteins revealed by RNA-dependent thermal proteome profiling. https://doi.org/10.64898/2026.07.15.738841

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