Zeb2 DNA-binding sites in ES cell derived neuroprogenitor cells reveal autoregulation and align with neurodevelopmental knockout mouse and disease phenotypes

Perturbation and mechanistic studies have shown that the DNA-binding transcription factor Zeb2 controls cell fate decision, differentiation and/or maturation in multiple cell lineages in embryos and after birth. In cultured embryonic stem cells (ESCs) Zeb2’s strong upregulation is necessary for their exit from primed pluripotency and entering neural and general differentiation. We engineered mouse ESCs to produce epitope-tagged Zeb2 from one of its two endogenous alleles. Using crosslinking ChIP-sequencing, we mapped for the first time 2,432 DNA-binding sites of Zeb2 in ESC-derived neuroprogenitor cells (NPCs). A new, major site maps promoter-proximal to Zeb2 itself, and its homozygous removal demonstrates that Zeb2 autoregulation is necessary to elicit proper Zeb2 effects in ESC→NPC differentiation. We then cross-referenced all Zeb2 DNA-binding sites with transcriptome data from Zeb2 perturbations in ESCs, ventral forebrain in mouse embryos, and adult neurogenesis. While the characteristics of these neurodevelopmental systems differ, we find interesting overlaps. Collectively, these new results obtained in ESC-derived NPCs significantly add to Zeb2’s role as neurodevelopmental regulator as well as the causal gene in Mowat-Wilson Syndrome. Also, Zeb2 was found to map to loci mutated in other human congenital syndromes, making variant or disturbed levels of ZEB2 a candidate modifier principle in these. Significance statement Zeb2 is needed for exit from primed pluripotency and differentiation of ESCs and being studied in various cell lineages and tissues/organs in knockouts and adult mice. Phenotyping has mainly documented transcriptomes of Zeb2-mutant affected cell types, but ChIP-seq data are still not available to document Zeb2’s direct target loci as repressor or activator of transcription. This study maps for the first time the Zeb2 genome-wide binding sites in ESC-derived neuroprogenitors, and discovered Zeb2 autoregulation. Cross-referencing these ChIP-seq data with transcriptome profiles of Zeb2 perturbation further explains Mowat-Wilson Syndrome defects and proposes ZEB2 as candidate modifier gene in other syndromes. ### Competing Interest Statement The authors have declared no competing interest.