High-throughput identification of dominant negative polypeptides in yeast

Dominant negative polypeptides can act as inhibitors by binding to the wild type protein or by titrating an essential ligand. Here, we use high-throughput sequencing of DNA libraries composed of fragments of yeast genes to identify dominant negative polypeptides based on their depletion during cell growth. The method uncovers numerous inhibitory polypeptides for a protein and thus is capable of defining interacting domains with exquisite resolution, even pinpointing individual residues that contact ligands.