A scalable Tn5-based method for genome-wide DNA methylation profiling in development and disease

Abstract DNA methylation is a key epigenetic modification involved in development and disease, including cancer, and serves as a biomarker for diagnosis. Current detection methods, such as bisulfite sequencing, provide base-pair resolution but require high sequencing depth and cost. Here, we developed C me CUT&Tag, a Tn5-based approach that uses methylation-binding domain fusion proteins to selectively target methylated DNA in chromatinized and isolated DNA. This enables adapter insertion into methylated regions, allowing low-depth sequencing for quantitative analysis or optional cytosine conversion for base-pair resolution. C me CUT&Tag enables genome-wide DNA methylation profiling with reduced input and sequencing requirements. We demonstrate its performance in characterizing DNA methylation across development and disease in human stem cells, organoids, zebrafish embryogenesis, and tumor biopsies. The method shows strong concordance with bisulfite sequencing and supports the classification of brain tumor samples into methylation subtypes. These features make C me CUT&Tag a scalable and cost-effective approach for epigenetic research and potential clinical applications.