CDX1 is a transcription factor that plays a key role in intestinal development and differentiation. However, the downstream targets of CDX1 are less well defined than those of its close homologue, CDX2. We report here the identification of downstream targets of CDX1 using microarray gene-expression analysis and other approaches. Keratin 20 (KRT20), a member of the intermediate filament and a well-known marker of intestinal differentiation, was initially identified as one of the genes likely to be directly regulated by CDX1. CDX1 and KRT20 mRNA expression were significantly correlated in a panel of 38 colorectal cancer cell lines. Deletion and mutation analysis of the KRT20 promoter showed that the minimum regulatory region for the control of KRT20 expression by CDX1 is within 246 bp upstream of the KRT20 transcription start site. ChIP analysis confirmed that CDX1 binds to the predicted CDX elements in this region of the KRT20 promoter in vivo. In addition, immunohistochemistry showed expression of CDX1 parallels that of KRT20 in the normal crypt, which further supports their close relationship. In summary, our observations strongly imply that KRT20 is directly regulated by CDX1, and therefore suggest a role for CDX1 in maintaining differentiation in intestinal epithelial cells. Because a key feature of the development of a cancer is an unbalanced program of proliferation and differentiation, dysregulation of CDX1 may be an advantage for the development of a colorectal carcinoma. This could, therefore, explain the relatively frequent down regulation of CDX1 in colorectal carcinomas by hypermethylation.colorectal cancer ͉ epithelial ͉ cell lines ͉ methylation ͉ cancer stem cells M embers of the keratin family provide structural support for the cell. They are also involved in apoptosis and protect cells from stress (1). Mutations of some keratins lead to genetic diseases, for example, of the skin and the liver (2-4). Keratin 20 (KRT20), a member of the keratin family, has been cloned and classified as a type-I keratin with a highly conserved amino acid sequence (5). It is mainly expressed in the cytoplasm of epithelial cells in the small and large intestine and in Merkel cells of the skin (5). As KRT20 is expressed in the epithelial cells of the crypt, it has been widely studied as a marker of differentiation in normal epithelium and colorectal cancer (CRC) samples (6-9). Previous studies have suggested that KRT20 is phosphorylated in association with mucin secretion and filament organization (10, 11). Transgenic mice with mutations at a conserved Arg to His site (R80H) show collapse of intermediate filaments.Despite its clearly important functions in the intestine, little is known about the regulation of KRT20.CDX1 is a homeobox transcription factor that is important for intestinal development and is specifically expressed in the small and large intestine in both mice and humans (12-15). CDX1 plays a role in intestinal epithelial cell differentiation (16) and is down-regulated in a number of CRC-derived cell lines...