Single Cell Epigenetic Profiling

Single-cell epigenetic profiling has rapidly advanced our ability to study gene regulation by resolving chromatin features at the level of individual cells. Whereas bulk assays obscure critical regulatory differences across heterogeneous tissues, methods such as single-cell CUT&Tag now enable precise mapping of histone modifications, transcription factor binding, and other chromatin-associated proteins with high signal-to-noise and minimal input requirements. These approaches provide a detailed view of epigenetic states underlying development, disease progression, and responses to external stimuli, offering insights that cannot be captured through conventional population-averaged measurements.

Building on these capabilities, Droplet Paired-tag integrates CUT&Tag with single-cell RNA sequencing, simultaneously capturing chromatin marks and transcriptional output from the same nucleus. This combined modality allows researchers to distinguish active, repressed, and transitional regulatory states, identify rare or previously uncharacterized cell populations, and directly link chromatin architecture to gene expression. By outlining the principles, workflows, quality metrics, and applications of these technologies, this white paper provides a practical primer for researchers seeking to apply single-cell epigenetic methods to complex biological systems.

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