We have cloned the polyomavirus mutant fPyF9, which persists in an episomal state in F9 embryonal carcinoma cells (K. Ariizumi and H. Ariga, Mol. Cell. Biol. 6:3920-3927, 1986). fPyF9 carries three copies of exogenous sequences, the prototype of which is a 21-base-pair repeat (box DNA), in the region of the enhancer B domain of wild-type polyomavirus DNA. The consensus sequence, GCATTCCATTGTT, is 13 base pairs long. The box DNA inserted into fPyF9 appeared to come from a cellular sequence and was present in many kinds of DNAs, including F9 chromosomal DNA. The biological function of box DNA was analyzed by chloramphenicol acetyltransferase expression assays, using chimeric plasmids containing box DNA conjugated with simian virus 40 promoter elements. The results showed that box DNA repressed the activities both of the simian virus 40 promoter and enhancer only in transfected undifferentiated F9 cells and not in differentiated LTK-cells. Box DNA functioned independently of orientation and position with respect to the promoter in an enhancerlike manner, although the effect of box DNA was opposite that of the enhancer. The XhoI linker insertion into the consensus sequences of box DNA abolished the repression activity, and the protein(s) recognizing the consensus sequences was identified only in F9 cells, not in L cells. These analyses suggest that box DNA may be a negative regulatory element that functions in undifferentiated cells.Eucaryotic enhancer sequences play important roles in the regulation of a variety of viral and cellular genes (23). An enhancer is defined as an element that stimulates the level of transcription of a linked gene independently of position and orientation with respect to the promoter (23). It has recently been shown that many enhancers function in specific cells or tissues or in response to an inducing signal; the immunoglobulin heavy-chain gene enhancer functions only in B lymphocytes (4,14), and the expression of the cytochrome P1-450 gene is induced by dioxin (20).On the other hand, a negative enhancer has recently been discovered. This regulatory element functions in cis, and its mode of action is similar to that of a positive enhancer. This element, now called a silencer or dehancer, was initially discovered in the MAT locus of Saccharomyces cerevisiae, the locus that determines mating type (8). Furthermore, elements with similar properties have been shown to be located in upstream regions of the c-myc (26), p53 (7), and human 1-interferon (15) genes and in the long terminal repeat of human T-cell lymphotropic virus type III (27). Enhancers in the long terminal repeat (32, 33) and 1-interferon gene (15, 40), however, are also present close to the negative regulatory sequence. Both sequences appear to play a key role in transcriptional control of the gene linked to the 3' end. Cellular genes are generally thought to be cooperatively regulated by negative and positive enhancers, with the exception of a housekeeping gene such as the actin gene (34). To understand the mechanism of gene r...