The transcription factor ZBED6 (zinc finger, BED-type containing 6) is a repressor of IGF2 whose action impacts development, cell proliferation, and growth in placental mammals. In human colorectal cancers, IGF2 overexpression is mutually exclusive with somatic mutations in PI3K signaling components, providing genetic evidence for a role in the PI3K pathway. To understand the role of ZBED6 in tumorigenesis, we engineered and validated somatic cell ZBED6 knock-outs in the human colorectal cancer cell lines RKO and HCT116. Ablation of ZBED6 affected the cell cycle and led to increased growth rate in RKO cells but reduced growth in HCT116 cells. This striking difference was reflected in the transcriptome analyses, which revealed enrichment of cell-cycle-related processes among differentially expressed genes in both cell lines, but the direction of change often differed between the cell lines. ChIP sequencing analyses displayed enrichment of ZBED6 binding at genes up-regulated in ZBED6-knockout clones, consistent with the view that ZBED6 modulates gene expression primarily by repressing transcription. Ten differentially expressed genes were identified as putative direct gene targets, and their down-regulation by ZBED6 was validated experimentally. Eight of these genes were linked to the Wnt, Hippo, TGF-β, EGF receptor, or PI3K pathways, all involved in colorectal cancer development. The results of this study show that the effect of ZBED6 on tumor development depends on the genetic background and the transcriptional state of its target genes.C olorectal cancers (CRCs) are caused by sequential mutations in driver genes of key cellular systems such as the Wnt, EGFR/Ras/MAPK, PI3K, TGFB, and TP53 pathways (1). Somatic mutations in the PI3K pathway members PIK3CA and PTEN occur late in CRC progression and contribute to increased tumor cell growth and invasivity (2-4). In CRC, overexpression of IGF2 is mutually exclusive with activating genomic alterations of the PI3K pathway genes PIK3CA and PIK3R1 (5). Further, IRS2 overexpression is mutually exclusive with IGF2 overexpression. The IRS2 gene is frequently amplified in CRCs (5) and encodes a protein that links IGF1R, a receptor for IGF1 and IGF2, with PI3K signaling. The importance of this pathway in colorectal tumorigenesis motivates studies to understand its regulation better.The ZBED6 (zinc finger, BED-type containing 6) transcription factor is a recently discovered negative regulator of IGF2 expression (6, 7). The intronless ZBED6 gene encodes two N-terminal zinc finger BED domains (8) and an hAT (hobo-Ac-Tam3) dimerization domain. Based on its primary structure, ZBED6 belongs to the hAT transposase family (9). The ZBED6 gene is located in the first intron of ZC3H11A and is transcribed as a composite transcript from the ZC3H11A promoter. An SNP (rs4951011) located in the 5′ UTR of ZBED6 recently was found to be associated with breast cancer susceptibility in a genome-wide association study (10). In pigs, a G-to-A mutation in the highly conserved CpG island in the thi...