Molecular Determinants of Functional Bacterial sRNA-mRNA Interactions Revealed by Integrating RNA Interactomes and Interpretable Machine Learning

Abstract

Bacterial small RNAs (sRNAs) regulate gene expression by base pairing with target mRNAs, yet transcriptome-wide interactome mapping has shown that many sRNA-mRNA interactions detected in vivo have modest or no regulatory effect using orthogonal reporter assays. The features that determine functional outcome remain poorly defined. Here, we integrated Hfq-CLASH interactome mapping with matched transcriptomic and proteomic profiling in Escherichia coli and developed an interpretable machine-learning framework to identify the determinants that distinguish functional from non-functional interactions. Using sequence, structural, thermodynamic, duplex and protein-occupancy features, transcriptomic and proteomic responses were predicted with above-chance performance, achieving AUCs of 0.78 and 0.74, respectively. Feature attribution revealed that physical pairing alone is insufficient for regulation; instead, regulatory outcome is shaped by a coordinated interplay between RNA secondary structure, thermodynamic accessibility and local protein-binding context. Target-side Hfq occupancy emerged as a positive predictor of functional regulation, whereas AR2-domain occupancy on the sRNA was associated with non-responsive interactions, suggesting that distinct ribonucleoprotein states may separate productive regulation from non-productive binding. These findings indicate that the regulatory fate of an sRNA-mRNA interaction is an emergent property of its biophysical context and protein-binding environment, rather than a direct consequence of physical pairing alone.