ATAC-Me captures spatiotemporal dynamics of DNA methylation across the chromatin accessible genome

DNA methylation of enhancers is dynamic, cell-type specific, and vital for cell fate progression. However, current models inadequately define its role within the highly ordered steps of gene regulation. An analysis of independent datasets show an unanticipated overlap between DNA methylation and chromatin accessibility at enhancers of steady state stem cells, suggesting that two opposing features might exist concurrently. To temporally define the relationship between these two events, we developed ATAC-Me, which probes accessibility and methylation from a single library preparation. We identified waves of accessibility, both transient and persistent, occurring rapidly across thousands of myeloid enhancers as monocyte cells transition to a macrophage state. Persistent methylation states were observed at a majority of these sites while transcriptional responses of nearby genes tracked closely with accessibility. ATAC-Me uncovers a significant disconnect between chromatin accessibility, DNA methylation status, and gene activity. This unexpected observation highlights the value of ATAC-Me in constructing precise molecular timelines for understanding the role of DNA methylation in gene regulation. RNA-seq and ATAC-Me-seq libraries were generated for 5 time points of PMA stimulated THP-1 monocytes (0, 0.5, 1, 2, 24hrs), in biological replicate. Standard ATAC-seq libraries were generated at two time points (0, 24hr) in biological replicate. WGBS libraries were generated at two time points (0, 24 hr).