23 / 2026-03-09 17:35:07

Methyl-metabolite depletion relaxes 3D genome structures and facilitates totipotent reprogramming

methyl-donor inhibition,3D genome,totipotent reprogramming,DNA methylation,chromatin relaxation

The three-dimensional (3D) genome structure is essential for regulating gene expression and determining cell fate. While the stability of the 3D genome is paramount for maintaining cellular identity, this same stability can become a significant impediment during cell fate transitions. In this study, we use the mouse totipotent-like stem cell induction system to dissect the role of methyl-donor metabolism in 3D genome remodeling and cell fate transition. We hypothesize that methyl-donor inhibitors enhance stem cell reprogramming by dismantling the established 3D genome architecture, thereby lowering the epigenetic barrier to a totipotent state. We demonstrate that inhibiting methyl-donor pathways not only promotes the efficiency of totipotent potential stem cells (TPS) reprogramming but also induces a global relaxation of the 3D genome structures. This is characterized by a loosening of chromatin, a weakening of A/B compartmentalization, and a reduction in the strength and clarity of TAD boundaries and loop structures. We find that the genomic regions susceptible to this structural remodeling are significantly enriched for genes and pathways related to embryonic development and cell fate determination. These findings support a model in which methyl-donor inhibitors facilitate the transition to a totipotent-like state by creating a more plastic and permissive 3D genome landscape, effectively recapitulating a key feature of early embryonic development. This work provides a novel mechanistic insight into chemical reprogramming, linking cellular metabolism to the physical organization of the genome, and suggests that targeting 3D chromatin architecture could be a powerful strategy for advancing regenerative medicine.