Negative regulation of the human polyomavirus BK enhancer involves cell-specific interaction with a nuclear repressor

We have examined the cell type-specific regulation of the human BK virus (BKV) enhancer. This enhancer functions efficiently in cis to activate expression from the adenovirus major late promoter in the human kidney cell line, 293, and in a monkey kidney cell line, MK2, but not in the HeLa cell line. In gel retardation migration assays, specific BKV enhancer-protein complexes could be observed by using nuclear extracts prepared from each cell line. Moreover, a unique DNA-protein complex was observed by using the HeLa cell nuclear extracts. By DNase footprint analysis, four binding regions for HeLa cell nuclear proteins were defined within the BKV enhancer repeat region. Two of the protected regions encompassed nuclear factor 1 or CCAAT transcription factor binding sites. These nuclear factor 1 sites also were protected by nuclear proteins from the 293 and MK2 cell lines. The other two protected sites encompassed a region of symmetry which included a sequence similar to the simian virus 40 TC enhancer motif and to a conserved sequence present upstream or within the introns of several cellular genes. These two sites were not protected by either the 293 or MK2 nuclear proteins. Competition studies in transfected cells indicated that the reduced activity of the BKV enhancer in the HeLa cell line was due to negative regulation. Further, we have demonstrated that binding of a nuclear factor(s) to the HeLa cell-specific site is involved in the repression of enhancer activity.