ATAC-Me Captures Prolonged DNA Methylation of Dynamic Chromatin Accessibility Loci during Cell Fate Transitions

DNA methylation of enhancers is dynamic, cell-type specific, and vital for cell fate progression. However, current models inadequately define its role within the hierarchy of gene regulation. Analysis of independent datasets shows an unanticipated overlap between DNA methylation and chromatin accessibility at enhancers of steady-state stem cells, suggesting that these two opposing features might exist concurrently. To define their temporal relationship, we developed ATAC-Me, which probes accessibility and methylation from single DNA library preparations. We identified waves of accessibility occurring rapidly across thousands of myeloid enhancers in a monocyte-to-macrophage cell fate model. Prolonged methylation states were observed at a majority of these sites, while transcription 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. [Display omitted] •ATAC-Me simultaneously measures chromatin accessibility and DNA methylation (DNAme)•Enhancer accessibility and DNAme change independently during cell fate transitions•Loss of DNAme is delayed in nascent open chromatin regions•Transcriptional changes track with new enhancer accessibility despite prolonged DNAme Barnett et al. describe ATAC-Me, an approach that captures chromatin accessibility and DNA methylation simultaneously from a single DNA fragment library. ATAC-Me was used to probe temporal relationships between epigenetic and gene regulatory changes at enhancers during myeloid differentiation of THP1 monocytes, revealing a decoupling of chromatin and DNA methylation changes at transitioning enhancers.