InteractORF, predictions of human sORF functions from an interactome study
Short open reading frames (sORFs) are widespread yet often poorly annotated, and an increasing number are known to encode functional sORF-encoded peptides (sPEPs, or microproteins). Here, we use a system approach to determine the functions of sPEPs in three tissues: monocytes, skeletal muscle and brain. We first predicted interactions between sPEPs and canonical proteins and characterized their interaction interfaces. sPEPs preferentially target specific canonical partners rather than interacting promiscuously, and two functional groups emerge from their interaction features. A small subset (~2%) exhibits canonical protein-like features, with structured domains interacting with diverse proteins involved in tissue-specific functions. In contrast, most sPEPs contain short linear motifs with extensive phosphorylation potential, suggesting they may be involved in signaling. We then constructed the first sPEP-containing interactome networks and infer sPEP functions from network topology. Most sPEPs appear to act as regulatory elements modulating diverse cellular processes rather than acting directly as functional components. Knowledge-based validations using characterized sPEPs, show that our framework can capture context-specific functions beyond current annotations. Together with their limited evolutionary constraint, the pervasive regulatory roles of sPEPs suggest that they constitute a reservoir of functional novelty and an evolutionarily flexible layer of cellular regulation.