DNMT3A-dependent DNA methylation shapes the endothelial enhancer landscape

DNA methylation plays a fundamental role in regulating transcription during development, cell differentiation, and maintenance of cellular identity. However, the functional role of DNA methylation in the regulation of endothelial cell (EC) transcription during state transition, meaning the switch from an angiogenic to a quiescent cell state, has not been determined. Here, we conducted a DNA methylome analysis over a longitudinal postnatal timeline of EC in the murine pulmonary vasculature, revealing two significant observations. First, prominent alterations in DNA methylation patterns occurred during the transition from angiogenic to quiescent EC. Second, once a quiescent state is established, DNA methylation marks remain stable throughout further EC aging. These longitudinal differentially methylated regions correlated with endothelial gene expression and provided evidence for the recruitment of de novo DNA methyltransferase 3a (DNMT3A). Comprehensive loss-of-function studies in mice revealed that the absence of DNMT3A-dependent DNA methylation led to the loss of active enhancers, resulting in mild transcriptional changes, likely due to loss of active enhancer integrity. These results underline the importance of DNA methylation as a key epigenetic mechanism of EC function during state transition. Furthermore, we showed that DNMT3A-dependent DNA methylation appears to be involved in establishing the proper histone landscape required for accurate transcriptome regulation.