Background:The role of foxc1a in zebrafish somitogenesis remains elusive. Results: Zebrafish foxc1a knock-out embryos exhibit defective somites at early development. foxc1a works on the top of the genetic hierarchy of RA, Fgf, and Notch signaling network to regulate myod1 expression. Conclusion: Foxc1a controls zebrafish early somitogenesis by directly restricting aldh1a2 expression. Significance: The results reveal the genetic role of foxc1a in zebrafish early somitogenesis.

Transcription factors play crucial roles in patterning posterior neuroectoderm. Previously, zinc finger transcription factor was reported to be expressed in the posterior neuroectoderm of zebrafish embryos. However, its roles remain unknown. Here, we report that there are 13 copies of in the zebrafish genome, and all the paralogues share highly identical protein sequences and cDNA sequences. When are knocked down using a morpholino to inhibit their translation or dCas9-Eve to inhibit their transcription, the zebrafish gastrula displays reduced expression of, the marker gene for the posterior neuroectoderm. Further analyses reveal that diminishing produces the decreased expressions of, whereas overexpression of effectively rescues the reduced expression of in the posterior neuroectoderm. Additionally, knocking down causes the reduced expression of, a direct regulator of , in the posterior neuroectoderm, and overexpression of rescues the expression of in the knockdown embryos. In contrast, knocking down either or does not affect the expressions of Taken together, our results demonstrate that zebrafish control the expression of in the posterior neuroectoderm by acting upstream of and .

Engineered endonucleases are a powerful tool for editing DNA. However, sequence preferences may limit their application. We engineer a structure-guided endonuclease (SGN) composed of flap endonuclease-1 (FEN-1), which recognizes the 3′ flap structure, and the cleavage domain of Fok I (Fn1), which cleaves DNA strands. The SGN recognizes the target DNA on the basis of the 3′ flap structure formed between the target and the guide DNA (gDNA) and cut the target through its Fn1 dimerization. Our results show that the SGN, guided by a pair of gDNAs, cleaves transgenic reporter gene and endogenous genes in zebrafish embryonic genome.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1038-5) contains supplementary material, which is available to authorized users.