Genome-wide identification of Wnt/β-catenin transcriptional targets during Xenopus gastrulation

•21 novel transcriptional targets of Wnt/β-catenin are identified.•Targets are identified by combining transcriptome analysis as well as genome wide binding of β-catenin.•Most transcriptional targets display similar expression pattern to that of wnt8 during gastrulation.

The canonical Wnt/β-catenin signaling pathway plays multiple roles during Xenopus gastrulation, including posteriorization of the neural plate, patterning of the mesoderm, and induction of the neural crest. Wnt signaling stabilizes β-catenin, which then activates target genes. However, few targets of this signaling pathway that mediate early developmental processes are known. Here we sought to identify transcriptional targets of the Wnt/β-catenin signaling pathway using a genome-wide approach. We selected putative targets using the criteria of reduced expression upon zygotic Wnt knockdown, β-catenin binding within 50 kb of the gene, and expression in tissues that receive Wnt signaling. Using these criteria, we found 21 novel direct transcriptional targets of Wnt/β-catenin signaling during gastrulation and in addition have identified putative regulatory elements for further characterization in future studies.