Detecting Protein-DNA Binding in Single Molecules using Antibody Guided Methylation

Characterization of DNA binding sites for transcription factors and other proteins is of fundamental importance in molecular biology. It is commonly addressed experimentally by chromatin immunoprecipitation and sequencing (ChIP-seq) of bulk samples (103-107 cells). We have developed an alternative method that uses a Chromatin Antibody-mediated Methylating Protein (ChAMP), a GpC methyltransferase fused to protein G. By tethering ChAMP to a primary antibody directed against the DNA-binding protein of interest, and selectively switching on its enzymatic activity in situ, we generated distinct and identifiable methylation patterns next to the protein binding sites. This method is compatible with methods of single-cell methylation-detection and single molecule methylation identification. Indeed, as every binding event generates multiple nearby methylations, we were able to confidently detect protein binding sites in single cells and from single molecules.