N6-methyladenine in DNA antagonizes SATB1 in early development [ATAC-seq]

The recent discovery of N6-methyladenine (N6-mA) in mammalian genomes suggests that it may serve as an epigenetic regulatory mechanism. However, the biological role of N6-mA and the molecular pathways that exert its function remain unclear. Here we show that N6-mA has a key role in changing the epigenetic landscape during cell fate transitions in early development. We found that N6-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 N6-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 N6-mA also antagonizes SATB1 function in vivo by preventing its binding to chromatin. Concordantly, N6-mA functions at the boundaries between euchromatin and heterochromatin to restrict the spread of euchromatin. Repression of SIDD–SATB1 interactions mediated by N6-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 N6-mA function via SATB1, and reveal connections between DNA modification, DNA secondary structures and large chromatin domains in early embryonic development. ATAC-seq following Alkbh1 overexpression in embryonic stem cells

近期在哺乳动物基因组中发现的N6-甲基腺嘌呤（N6-methyladenine，N6-mA）提示其可能作为一种表观遗传调控机制发挥作用。然而，N6-mA的生物学功能及其发挥功能的分子通路仍不明确。本研究表明，N6-mA在早期发育过程中的细胞命运转变阶段，对重塑表观遗传景观具有关键作用。我们发现，在小鼠滋养层干细胞的发育过程中，N6-mA在应激诱导DNA双螺旋解稳定区（stress-induced DNA double helix destabilization，SIDD）区域特异性上调。SIDD区域易受拓扑应力诱导发生双螺旋解旋，在大规模染色质结构的组装中发挥关键作用。我们证实，N6-mA的存在可使SIDD与SATB1（一种可与SIDD区域结合的关键染色质组织者）之间的体外相互作用降低超过500倍。N6-mA的沉积还可通过阻止SATB1与染色质结合，在体内拮抗其功能。与此一致的是，N6-mA在常染色质与异染色质的边界处发挥功能，以限制常染色质的扩散。在细胞培养模型与体内环境中，由N6-mA介导的SIDD-SATB1相互作用抑制，对于滋养层发育过程中的基因调控至关重要。总体而言，我们的研究发现揭示了N6-mA通过SATB1发挥功能的一种意想不到的分子机制，并阐明了DNA修饰、DNA二级结构与早期胚胎发育中大规模染色质结构域之间的关联。本数据集包含胚胎干细胞过表达Alkbh1后的ATAC测序（ATAC-seq）数据。