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Background  The application of antisense molecules, such as morpholino oligonucleotides, is an efficient method of gene inactivation in vivo. We recently introduced phosphonic ester modified peptide nucleic acids (PNA) for in vivo loss-of-function experiments in medaka embryos. Here we tested novel modifications of the PNA backbone to knockdown the medaka  tcf3  gene.    Results  A single  tcf3  gene exists in the medaka genome and its inactivation strongly affected eye development of the embryos, leading to size reduction and anophthalmia in severe cases. The function of Tcf3 strongly depends on co-repressor interactions. We found interactions with Groucho/Tle proteins to be most important for eye development. Using a dominant negative approach for combined inactivation of all  groucho/tle  genes also resulted in eye phenotypes, as did interference with three individual  tle  genes.    Conclusions  Our results show that side chain modified PNAs come close to the knockdown efficiency of morpholino oligonucleotides in vivo. A single medaka  tcf3  gene combines the function of the two zebrafish paralogs  hdl  and  tcf3b . In combination with Groucho/Tle corepressor proteins Tcf3 acts in anterior development and is critical for eye formation.    Electronic supplementary material  The online version of this article (10.1186/s12896-017-0411-0) contains supplementary material, which is available to authorized users.

The function of tcf3 in medaka embryos: efficient knockdown with pePNAs