Genomics

A Tribe for RNA

Cell 165, 742–753 (2016)

Credit: ELSEVIER

Although the cross-linking and immunoprecipitation approach (CLIP) has been used to find targets of RNA-binding proteins (RBPs) in cells, the application of this method to identify cell-type-specific RBP targets in vivo remains limited because of the large amount of cellular material required. McMahon et al. developed a method called TRIBE (targets of RNA-binding proteins identified by editing) that allows cell-specific identification of RBP–RNA complexes in Drosophila using small amounts of RNA. They coupled an RBP to the catalytic domain of the RNA-editing enzyme ADAR that converts adenosine to inosine, which is subsequently read as guanosine. These editing events can be identified through RNA sequencing and bioinformatics analysis. As an example, the authors used TRIBE to identify targets of an RBP, Hrp48, and confirmed the detection of the same known RNA targets as for CLIP analysis in a Drosophila cell culture line. Hrp48-TRIBE was then expressed in Drosophila neuronal cell types ranging from dopaminergic neurons (containing 1,000 cells) to the small circadian PDF-neuropeptide-expressing cells (16 cells). In addition to detecting Hrp48 targets found in all neuronal cell types, McMahon et al. also identified unique cell-type-specific Hrp48 targets, which will prompt further analysis. Taken together, these results validate TRIBE as a useful tool that will help unravel the riboproteome of individual cell types.

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Miura, G. A Tribe for RNA. Nat Chem Biol 12, 387 (2016). https://doi.org/10.1038/nchembio.2092

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