Switch-TRIBE: Lineage-specific high-resolution profiling of endogenous RNA-protein interactions

RNA-binding proteins (RBPs) play vital roles in regulation of cell fate and function. Here, we introduce Switch-TRIBE, which conditionally tags endogenous RBPs with the adenosine deaminase catalytic domain to detect physiological RBP-RNA interactions. We apply Switch-TRIBE to the TRIM-NHL RBPs, BRAT and MEI-P26, essential regulators of Drosophila neurogenesis. Single-cell Switch-TRIBE in neural stem cell lineages defines cell-type specific targets and identifies novel neurogenesis regulators. Beyond target identification, Switch-TRIBE highlights the complex interplay between co-regulating RBPs, uncovering distinct binding site topographies. Our analysis uncovers a potential strategy used by BRAT and MEI-P26 to regulate lineage growth through direct binding of transcripts that encode the core metabolic and translation machineries. Switch-TRIBE provides a robust tool for characterizing RBP-RNA interactions in complex systems without compromising biological fidelity.