N(6)-methyladenine in DNA antagonizes SATB1 in early development

The recent discovery of N(6)-mA in mammalian genomes suggests that it may serve as an epigenetic regulatory mechanism(1). However, the biological role of N(6)-mA and molecular pathways exerting its function remain elusive. Herein, we demonstrate that N(6)-mA plays a critical role in changing the epigenetic landscape during cell fate transitions in early development. We found that N(6)-mA is upregulated during trophoblast stem cell development, specifically at Stress Induced DNA Double Helix Destabilization (SIDD) regions(2-4). It is well-known that SIDD regions are conducive to topological stress-induced double helix unpairing and play critical roles in organizing large-scale chromatin structures(3,5,6). We demonstrated that the presence of N(6)-mA abolishes (>500-fold) the in vitro interactions between SIDD and SATB1, a critical chromatin organizer interacting with SIDD regions; N(6)-mA deposition also effectively antagonizes SATB1 function in vivo by preventing its binding to chromatin. Concordantly, N(6)-mA functions at the boundaries between eu-/hetero- chromatin to restrict the spreading of euchromatin. N(6)-mA mediated repression is critical for gene regulation during trophoblast development in cell culture models and in vivo. Overall, our study discovers an unexpected molecular mechanism for N(6)-mA function via SATB1, and reveals surprising connections between DNA modification, DNA secondary structures and large chromatin domains in early embryonic development.