We profiled PBMCs from two donors using Cut&Tag and Droplet Paired-Tag, generating over 70,000 single-cell profiles. We identified hundreds of thousands of cisregulatory elements (cCREs), primarily repressive, active, or bivalent. Most cCREs were shared across immune cell types, with a few hundred defining subtypes. Single-cell data confirmed bivalency at specific loci and showed strong correlation with bulk Cut&Tag. These epigenetic landscapes in brain and PBMCs enhance our understanding of immune cell regulation and heterogeneity, revealing the mechanisms that define immune cell identity and function.

Single-cell epigenetic profiling identifies key biomarkers of cellular dysfunction and disease. Our methods simultaneously assess RNA expression and histone modifications in individual brain cells and PBMCs, providing high-quality, reproducible data. We discovered novel cell-type-specific cis-regulatory elements (cCREs) and heritability factors linked to Alzheimer's Disease (AD). Additionally, our approach enables the identification of aging and disease-related biomarkers, offering insights into their epigenetic mechanisms. These findings support the development of diagnostic tools and targeted therapies, advancing the understanding and treatment of complex health conditions.

Applying Paired-Tag to Alzheimer's neurons, we aligned with RNA data and identified shared pathologies. AD neurons showed H3K9me3 repression of genes essential for neuronal identity and synapses, linked to inflammation and dysfunction. Our single-cell epigenomic and transcriptomic analysis reveals specific cellular changes and therapeutic targets, demonstrating Paired-Tag’s effectiveness in understanding and treating complex diseases.