Nodal cis-regulatory elements reveal epiblast and primitive endoderm heterogeneity in the peri-implantation mouse embryo

► Ancestral mechanisms of Nodal regulation are conserved in the mouse blastocyst. ► Canonical Wnt signaling is activated in the epiblast before implantation. ► Activin/Nodal signaling is independent of Nodal and FoxH1 in mouse blastocysts. ► Activin/Nodal signaling is inversely correlated to Nanog presence in late blastocysts.