Mouse Embryonic Stem Cells Require Sustained DNMT1-Mediated DNA Methylation Maintenance for Epigenomic, Genomic and Functional Integrity

Abstract

SUMMARYOur research is motivated by the pivotal role of DNMT1 in maintaining DNA methylation, genomic stability, transposable element silencing, and imprinting alongside the extensive utilization of embryonic stem cells (ESCs) for modeling development and disease. Previously, we showed that DNA hypomethylation persisted throughoutDnmt1inactivation and rescue in mouse ESCs (mESCs), demonstrating their need for sustained DNMT1 activity. Here, expanding on our previous work, we assessed the broader epigenomic impact using EM-seq for enhanced DNA methylation coverage and sensitivity, ChIP-seq for five histone modifications and differential gene expression analysis, revealing dynamic epigenomic remodeling. We uncovered 20 regions with imprinted-like signatures and observed permanent de-repression of MERVL and MT2 transposable elements potentially associated with gene transcript chimerism. Genomic instability, cellular dysfunction, and lasting effects upon differentiation into germ layer lineages were also detected. Our findings enlighten DNMT1-dependent mechanisms in mESCs, offering foundational insights into developmental biology, disease pathogenesis and regenerative medicine.GRAPHICAL ABSTRACTHIGHLIGHTSEpigenomic stress induced byDnmt1inactivation in mESCs persists afterDnmt1rescueIdentification of 20 regions with imprinted-like epigenetic and regulatory signaturesMERVL and MT2 LTR de-repression with evidence of related gene transcript chimerismGenomic instability, cellular dysfunction, and lasting effects upon differentiation