BackgroundRecent　research　has　indicated　a　close　connection　between　the　three-dimensional　(3D)　structure　of　chromatin　and　early　embryo　development,　with　precise　higher-order　chromatin　folding　playing　a　significant　role　in　mediating　gene　expression.　However,　the　specific　role　of　3D　genomic　hierarchical　structure　and　its　dynamics　in　early　embryo　development　remains　largely　unknown.ResultsIn　this　study,　we　examined　the　hierarchical　topological　association　domain　(TAD)　during　early　embryo　development　and　its　relationship　with　zygotic　gene　activation　(ZGA),　gene　expression,　and　chromatin　accessibility　to　gain　a　better　understanding　of　the　dynamics　of　TAD　nesting　levels　during　this　developmental　stage.　Our　findings　show　that　ZGA　precedes　the　establishment　of　hierarchical　TAD,　leading　to　widespread　gene　expression,　an　increase　in　the　percentage　of　high-level　TAD　structures,　and　enhanced　chromatin　accessibility　at　higher　hierarchical　levels.　Additionally,　we　utilized　a　deep　neural　network　to　investigate　the　formation　of　TAD　boundaries　and　found　that　histone　H3　lysine　4　trimethylation　(H3K4me3)　and　histone　H3　lysine　trimethylation　(H3K27me3)　are　key　features　in　the　establishment　of　TAD　boundaries.　Furthermore,　we　observed　heterogeneous　dynamics　of　hierarchical　TAD　among　different　species.ConclusionsOverall,　our　study　sheds　light　on　the　folding　dynamics　of　hierarchical　TADs　during　early　embryo　development　and　underscores　their　close　relationship　with　transcriptional　programs.