Abstract
DNA methylation and histone modifications are critical epigenetic regulators that orchestrate gene expression and modulate various physiological and pathological processes. However, existing methodologies for simultaneous profiling of these epigenetic marks often require high cell input and suffer from data loss due to bisulfite conversion. In this study, we present advanced multimodal chromatin profiling methods, MethylTag and Multi-MethylTag, that address these challenges by integrating Tn5 transposase with methylated adaptors and optimizing postbisulfite library preparation. These methods enable high-resolution, multidimensional chromatin profiling with reduced cell input and improved data integrity. We validated these techniques in various human and mouse cell lines, revealing complex interactions between DNA methylation and histone modifications. Our findings highlight the utility of these approaches in enhancing epigenetic research and deepening our understanding of the regulatory mechanisms underlying gene expression.