Two promoter-specific host factors interact with adjacent sequences in an EIA-inducible adenovirus promoter

We previously reported the identification of a host factor (EIIA-EF) specific for an upstream transcriptional control sequence (-82 to -66) of the EIA-inducible adenovirus EIIA early promoter. The levels of this factor remained unchanged after virus infection of human cells. Another study also identified a factor (EIIF) specific for this same promoter, but the activity of this second factor was shown to increase severalfold after virus infection. We now show that these dramatically different results, both based on gel shift assays on the same promoter, may be explained by variations in protocol details and actually identify two distinct factors. When synthetic DNA copolymers [poly(dI).poly(dC) or poly(dI-dC).poly(dI-dC)] are used as competitors in gel shift assays, a factor specific for DNA sequences between -82 and -66 can be identified, whereas when natural eukaryotic DNAs (salmon sperm or calf thymus) are used as competitors a different factor specific for DNA sequences between -69 and -33 can be identified. We have mapped the DNA-protein contact residues for the EIIF by analyzing a series of linker scan mutants in gel shift assays and methylation interference experiments. The EIIA-EF and EIIF bind to two distinct but adjacent sequences. Competition experiments indicate that these two activities are due to two different factors. Consistent with the earlier reports, the levels of one (EIIA-EF) do not change after virus infection of human cells, whereas the levels of the other (EIIF) are increased severalfold.