Significance The small size of short ORF-encoded peptides (SEPs) has made it difficult to identify their cellular binding partners using standard methods. Here, we show that the photo-crosslinking amino acid AbK can be incorporated into overexpressed, epitope-tagged SEP transgenes, allowing covalent bond formation between SEPs and their interactors in live cells. From an AP-MS–based screen of conserved mammalian SEPs, we identified short ORF-encoded histone binding protein (SEBHP), a micropeptide which acts as a transcriptional regulator, capable of modulating more than 15% of the active transcriptome. The methodology described herein will likely be of broad utility in annotating the essential physiological roles of SEPs.