WT1, a critical regulator of kidney development, is a tumor suppressor for nephroblastoma but in some contexts functions as an oncogene. A limited number of direct transcriptional targets of WT1 have been identified to explain its complex roles in tumorigenesis and organogenesis. In this study we performed genome-wide screening for direct WT1 targets, using a combination of ChIP-ChIP and expression arrays. Promoter regions bound by WT1 were highly G-rich and resembled the sites for a number of other widely expressed transcription factors such as SP1, MAZ, and ZNF219. Genes directly regulated by WT1 were implicated in MAPK signaling, axon guidance, and Wnt pathways. Among directly bound and regulated genes by WT1, nine were identified in the Wnt signaling pathway, suggesting that WT1 modulates a subset of Wnt components and responsive genes by direct binding. To prove the biological importance of the interplay between WT1 and Wnt signaling, we showed that WT1 blocked the ability of Wnt8 to induce a secondary body axis during Xenopus embryonic development. WT1 inhibited TCF-mediated transcription activated by Wnt ligand, wild type and mutant, stabilized -catenin by preventing TCF4 loading onto a promoter. This was neither due to direct binding of WT1 to the TCF binding site nor to interaction between WT1 and TCF4, but by competition of WT1 and TCF4 for CBP. WT1 interference with Wnt signaling represents an important mode of its action relevant to the suppression of tumor growth and guidance of development.ChIP-ChIP ͉ microarray ͉ tumor suppressor T he genetic etiology of Wilms tumorigenesis is heterogeneous including loss-of-imprinting of IGF2 (1), deletions and mutations of WT1 (reviewed in ref.2) and the recently identified WTX (3) genes. In addition, somatic mutations in -catenin leading to a stabilized protein are found in 15% of cases and curiously almost all of these mutation cases are found in patients lacking functional WT1 alleles (4-7).The WT1 tumor suppressor gene encodes a zinc finger transcription factor, possibly yielding up to 32 different isoforms (8). The major isoforms differ in the presence or absence of amino acids KTS in the zinc finger region and the presence or absence of a 17-aa stretch in the middle of the protein. The ϪKTS isoforms have been linked to DNA binding-mediated transcriptional control whereas the ϩKTS isoforms have been implicated in RNA processing as well (9). Renal agenesis in the Wt1 knockout mouse and the presence of constitutional mutations in WT1 in a number of renal developmental syndromes indicate a critical role for WT1 in kidney development.