Dual role of ZIC2 during neural induction: from priming transcription factor to enhancer activator

Defects in ZIC2, a member of the Zinc Finger of the Cerebellum family of transcription factors (TFs), cause holoprosencephaly, a congenital brain malformation characterized by the defective cleavage of cerebral hemispheres. However, the gene regulatory network (GRN) controlled by ZIC2 during neural development remains largely unexplored. Here, we combined a mouse embryonic stem cell (mESC) in vitro differentiation model toward anterior neural progenitors with genome editing and genomic methods to elucidate the ZIC2 GRN. We found that ZIC2 is dispensable in mESC due to compensation by ZIC3. In contrast, during neural induction ZIC2 directly controls the expression of master regulators implicated in the patterning and morphogenesis of specific brain regions (e.g. midbrain and roof plate). Mechanistically, ZIC2 plays a dual role in neural differentiation: during pluripotency exit, ZIC2 binds de novo to distal enhancers and increases their chromatin accessibility; during neural induction, ZIC2 is essential for the activation of a subset of the previously primed enhancers, which in turn control the expression of neural patterning regulators and signalling pathways (i.e. WNT) that prevent premature neuronal differentiation. Therefore, by sequentially acting as a promiscuous priming TF and selective enhancer activator, ZIC2 canalizes pluripotent cells toward neural progenitors with rostro-dorsal identities.