notum1, acting downstream of pitx2, is essential for proper eye and craniofacial development.

Axenfeld-Rieger syndrome (ARS) is a rare autosomal dominant developmental disorder characterized by ocular anterior chamber anomalies with an increased risk of glaucoma and systemic defects. Mutations in the transcription factor PITX2 were the first identified genetic cause of ARS. Despite the developmental importance of PITX2 and its role in ARS, the pathways downstream of PITX2 have yet to be fully characterized. Comparative transcriptome analyses involving pitx2-enriched cell populations isolated via fluorescence activated cell sorting of tissues expressing (Tg(-2.6pitx2-CE4:GFP)) reporter in wild-type and pitx2M64* mutant zebrafish embryos identified the highly down-regulated target notum1b, an ortholog of human NOTUM encoding a secreted carboxylesterase that cleaves a necessary palmitoleate moiety from WNT proteins. Further experiments confirmed a decrease in notum1b and identified down-regulation of another NOTUM ortholog, notum1a, in the developing mutant eye. CRISPR-generated permanent double knockout zebrafish lines of notum1b and notum1a, notum1-/-, displayed defects in craniofacial and ocular development, including corneal defects, small lenses, increased sizes of the anterior and posterior chambers, and anomalies in teeth development. Analysis of head transcriptome of notum1-/- zebrafish in comparison to wild-type predicted an up-regulation of the WNT pathway. We present NOTUM/notum1 as an important factor in ocular and craniofacial development and a novel downstream member of the PITX2/pitx2 pathway.