Coordination of germ-layer lineage choice by TET1 during primed pluripotency (ChIP-seq)

Gastrulation in the early post-implantation stage mammalian embryo begins when epiblast cells ingress to form the primitive streak or develop as the embryonic ectoderm. The DNA dioxygenase Tet1 is highly expressed in the epiblast and yet continues to regulate lineage specification during gastrulation when its expression is diminished. Here, we show how Tet1 plays a pivotal role upstream of germ layer lineage bifurcation. During the transition from naive pluripotency to lineage priming, a global reconfiguration re-distributes Tet1 from Oct4 co-bound promoters to distal regulatory elements at lineage differentiation genes which are distinct from high-affinity sites engaged by Oct4. An altered chromatin landscape in Tet1-deficient primed epiblast-like cells is associated with enhanced Oct4 expression and binding to Nodal and Wnt target genes, resulting in collaborative signals that enhance mesendodermal and inhibit neuroectodermal gene expression during lineage segregation. A permissive role for Tet1 in neural fate induction involves Zic2-dependent engagement at neural target genes at lineage priming, is dependent on the signaling environment during gastrulation and impacts neural tube closure at post-gastrulation. Our findings provide mechanistic information for epigenetic integration of pluripotency and signal-induced differentiation cues. Overall design: Genome-wide binding profiles for Tet1 and Oct4 in 2iL-cultured embryonic stem cells (ESCs) and epiblast-like cells (EpiLCs).