Identification of Microprotein-Protein Interactions via APEX Tagging

Microproteins are peptides and small proteins encoded by small open reading frames (smORFs). Newer technologies have led to the recent discovery of hundreds to thousands of new microproteins. The biological functions of a few inicropioteins have been elucidated, and these micro-proteins have fundamental roles in biology ranging from limb development to muscle function, highlighting the Value of characterizing these molecules. The identification of microprotein protein interactions,(MPIs) has proven to be a successful approach to the functional characterization of these genes; however, traditional immunoprecipitation methods result in the, enrichment of nonspecific. interactions for, microproteins. Here, we test and apply an in situ proximity tagging method that relies on an engineered ascorbate peroxidase 2 (APEX) to elucidate MPls. The results,demonstrate that APEX tagging is superior. to traditional immunoprecipitation methods for microproteins. Furthermore,the application of APEX tagging to an uncharacterized microprotein called Cllorf98 revealed that this microprotein interacts with nucleolar proteins nucleophosmin and nucleolin, demonstrating the ability,of this approach to identify novel. hypothesis-generating MPIs.