Lineage-specific enhancer insertions regulate Prdm14 to drive the rapid transition from naïve to formative pluripotency in rodents

The network of transcription factors is dynamically reorganized during the transition from naïve to formative pluripotency. In mice, Prdm14 is expressed in naïve pluripotent cells but rapidly downregulated upon exit from the naïve state. In contrast, PRDM14 expression persists throughout pluripotency transitions in non-rodent mammals, including pigs and humans. Here, we investigate the molecular mechanisms underlying the rodent-specific expression of Prdm14. Using CRISPR/Cas9-mediated deletions, we demonstrated that OCT4 and TFCP2L1 recognition sequences within Muroidea-specific cis-regulatory elements located downstream of Prdm14 are essential for its transcriptional upregulation required for the upregulation of Prdm14 in naive embryonic stem cells (ESCs). Loss of these enhancers suppresses Pramel7 induction and impairs degradation of UHRF1, thereby attenuating global DNA demethylation under 2iL conditions. Moreover, deletion of PRDM14-binding motifs in Muroidea-specific enhancers disrupts its negative feedback loop, resulting in delayed transition from the naïve to formative pluripotent state. Overall design: RNA-seq experiments of WT, Cis KO of Prdm14, Prdm14-overexpressing embryonic stem cells