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bioRxiv · 10.64898/2026.02.23.707397

Graph-based RNA structural representation reveals determinants of subcellular localization

Hao, Y.·Sun, H.·Ran, Z.·Guo, X.·Liu, M.·Bi, Y.·Polo, J.·Liu, N.·Li, F.
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Abstract

RNA subcellular localization is a key determinant of RNA function and regulation, yet existing computational approaches rely primarily on sequence or simplified structural descriptors, limiting their scalability to long transcripts, their ability to model inter-label dependencies, and their applicability across RNA types. Here, we present GRASP, a unified graph neural network framework for predicting RNA subcellular localization using a heterogeneous graph representation that is RNA substructure-aware. GRASP presents each RNA as a multi-scale graph comprising nucleotide nodes and secondary-structure-derived substructure nodes, connected by relational edges, enabling joint modeling of base-level interactions and regional structural context. The model further incorporates multi-label dependency learning to capture co-localization patterns across cellular compartments within a unified framework. Across multiple benchmark datasets and RNA types, GRASP consistently outperforms state-of-the-art sequence-based and structure-informed methods, achieving substantial improvements in accuracy, F1 score, and AUC while maintaining strong scalability to long transcripts. In addition, the graph-based representation provides biologically interpretable insights into structural determinants of RNA localization. The source code and data are available at https://github.com/ABILiLab/GRASP, and the web server is accessible at http://grasp.biotools.bio.

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Hao, Y., Sun, H., Ran, Z., Guo, X., Liu, M., Bi, Y., Polo, J., Liu, N., Li, F.. 2026-02-24. Graph-based RNA structural representation reveals determinants of subcellular localization. https://doi.org/10.64898/2026.02.23.707397

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