Embryonic transcriptome analysis of wt vs irf6-/- zebrafish at 4hpf

We report transcriptional profiles of 4hpf zebrafish embryos from either wild-type or a CRISPR-targeted irf6 loss-of-function mutant. Irf6 is a transcription factor implicated in syndromic and nonsyndromic forms of cleft palate. To define critical genes involved in palate development, we harvested RNA from irf6-/- embryos before an embryonic lethal stage in zebrafish and carried out RNA-sequencing and subsequent analysis. We identify top differentially expressed genes that include genes involved in periderm development, genes expressed in developmental processes (such as Fgfs and Wnt-pathway genes), and genes involved in orofacial clefting. We identify a crucial gene esrp1 that we chose for further validation and downstream analysis. mRNA profiles of 4hpf wild-type or irf6-/- zebrafish embryos.