Single-cell and single-molecule profiling of protein-DNA interactions by MACHA

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Summary Protein-DNA interactions are fundamental to DNA-dependent processes such as transcription, replication, DNA repair, and chromosome organization in all domains of cellular life. Enrichment-based methods to detect protein-DNA interactions are widely used to obtain genome-wide high-resolution maps of transcription factor binding and chromatin states. However, these methods have severe shortcomings when applied to single cells. In single-cell applications, enrichment-based methods cannot distinguish between unbound DNA and unsuccessful recovery of protein-bound DNA since both lead to absent DNA fragments and the sparse data makes it difficult or impossible to obtain cell-type-resolved binding profiles of transcription factors starting from complex tissues. This limitation significantly reduces the information content of single-cell data. MACHA will detect protein-DNA interactions in cells as cytosine methylation catalyzed by an exogenous GpC methyltransferase (GpCMTase) that is directed to protein-bound DNA by a primary antibody recognizing the protein of interest.