MicroRNA miR-196a controls neural crest patterning by repressing immature neural ectoderm programs in Xenopus embryos

Neural crest (NC) cells form a multipotent stem cell population specified during neurulation, which undergo an epithelial-to-mesenchymal transition (EMT) and migrate extensively in the developing embryo, to generate numerous tissues and cell types including the craniofacial skeleton, the peripheral nervous system and pigment cells. The genetic and molecular details of NC specification are governed by a complex, yet still partially understood gene regulatory network (NC-GRN). In particular, the precise function of microRNAs (miRNA) in this network remains poorly characterized. MiRNAs are short non-coding 20–22 nucleotides long RNAs, which control gene expression through post-transcriptional repression. Since miRNA-196a is expressed in the developing neural and NC cells of Xenopus laevis embryos, we here investigated miR-196a function in the NC-GRN, by knocking-down its expression using antisense morpholinos. Depletion of miR-196a revealed major NC and craniofacial phenotypes. These defects were preceded by the perturbed expression of key neural, neural border and NC markers such as sox2/3, zic1/3, pax3, sox10 and snail2. Using RNA sequencing of individual neural border and NC explants, we have identified a signature of genes up- and down-regulated by miR-196a and validate these with rescue experiments using a miRNA mimic. Our study identifies miR-196a as a key actor of early patterning in the dorsal ectoderm, balancing the extent of immature neural plate progenitors with NC and placode specification, while also promoting neuron differentiation within the neural plate.