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

Traditional detection methods, such as bisulfite sequencing, offer base-pair resolution but are costly and require high sequencing depths. We developed CmeCUT&Tag, a novel approach using methylation-binding domain fusion proteins coupled to hyperactive Tn5 transposase that selectively targets methylated DNA regions in both chromatinized and isolated DNA.

These fusion proteins insert sequencing adapters into methylated regions, allowing low-depth sequencing for quantitative methylation assessment or bisulfite treatment for base pair resolution. Our approach enables comprehensive genome-wide DNA methylation profiling with minimal sequencing coverage. We demonstrated its efficacy in detecting DNA methylation in human stem cells and organoid systems.