N-methyladenine in DNA antagonizes SATB1 in early development.

The recent discovery of N-methyladenine (N-mA) in mammalian genomes suggests that it may serve as an epigenetic regulatory mechanism. However, the biological role of N-mA and the molecular pathways that exert its function remain unclear. Here we show that N-mA has a key role in changing the epigenetic landscape during cell fate transitions in early development. We found that N-mA is upregulated during the development of mouse trophoblast stem cells, specifically at regions of stress-induced DNA double helix destabilization (SIDD). Regions of SIDD are conducive to topological stress-induced unpairing of the double helix and have critical roles in organizing large-scale chromatin structures. We show that the presence of N-mA reduces the in vitro interactions by more than 500-fold between SIDD and SATB1, a crucial chromatin organizer that interacts with SIDD regions. Deposition of N-mA also antagonizes SATB1 function in vivo by preventing its binding to chromatin. Concordantly, N-mA functions at the boundaries between euchromatin and heterochromatin to restrict the spread of euchromatin. Repression of SIDD-SATB1 interactions mediated by N-mA is essential for gene regulation during trophoblast development in cell culture models and in vivo. Overall, our findings demonstrate an unexpected molecular mechanism for N-mA function via SATB1, and reveal connections between DNA modification, DNA secondary structures and large chromatin domains in early embryonic development.