Investigating DNA Methylation and Chromatin Accessibility Dynamics During Cell Fate Specification

Abstract

Epigenetic mechanisms govern the transcriptional activity of lineage-specifying enhancers; but recent work challenges the dogma that joint chromatin accessibility and DNA demethylation are prerequisites for transcription. To investigate DNA methylation function in dynamic processes, we developed and optimized ATAC-Me, a joint profiling method to measure DNA methylation and chromatin accessibility simultaneously. Through application of ATAC-Me, we established a highly-resolved timeline of DNA methylation and chromatin accessibility dynamics during neural progenitor cell differentiation. We discover that, while complete demethylation appears delayed relative to shorter-lived chromatin changes for thousands of enhancers, DNA demethylation actually initiates with 5-hydroxymethylation before appreciable accessibility and transcription factor occupancy is observed. The extended timeline of DNA demethylation creates temporal discordance appearing as epigenetic heterogeneity between these distinct layers of enhancer regulation. The gain of methylation is exceedingly rare and resulting enhancer hypomethylation persists long after chromatin activities have dissipated. We demonstrate that these timepoint specific methylation states predict past, present and future chromatin accessibility using machine learning models. Thus, chromatin and DNA methylation collaborate on different timescales to mediate short and long-term enhancer regulation during cell fate specification.