Uhrf1 loss alters Ctcf-mediated topological organization during early mouse embryogenesis

To define its function, we generated conditional Uhrf1 knockout embryonic stem cells (ESCs) and embryos. Uhrf1⁻/⁻ ESCs exhibited near-complete loss of 5mC and 5hmC but maintained pluripotency, whereas Uhrf1-null embryos developed normally until E8.5 and then failed to further develop by E9.5, phenocopying Dnmt1 loss.

Single-cell multi-omic (ME-seq) profiling of E8.5 embryos revealed impaired lineage stabilization, widespread hypomethylation, and disrupted chromatin architecture. Uhrf1 loss predicted altered CTCF occupancy, accompanied with disorganized enhancer-promoter interactions, and defective Bmp signaling, particularly within neural crest populations. These findings identify Uhrf1 as a central regulator tightly coupling DNA methylation maintenance to 3D genome organization during gastrulation to direct early lineage specification, positioning Uhrf1 as a pivotal mediator of epigenetic information transfer during early embryogenesis.