A novel sequence-specific DNA-binding protein, LCP-1, interacts with single-stranded DNA and differentially regulates early gene expression of the human neurotropic JC virus.

We have identified a novel brain-derived single-stranded-DNA-binding protein that interacts with a region of the human neurotropic JC virus enhancer designated the lytic control element (LCE). This nuclear factor, LCP-1 (for lytic control element-binding protein 1), specifically recognizes the LCE, as determined by gel retardation assays. Alkylation interference showed that specific nucleotides within the LCE were contacted by LCP-1. Subsequent experiments revealed that point mutations within the LCE differentially affected LCP-1 binding. UV cross-linking and competition analysis suggested that the LCP-1 DNA-protein complexes were 50 to 52 and 100 to 120 kDa in size. Promoter mutations that affected LCP-1 binding reduced early mRNA transcription during the early phase of the lytic cycle. However, upon DNA replication in the presence of JC virus T antigen, when early mRNA initiation shifts to new locations indicative of the late phase, the LCP-1 mutations had no effect. We suggest that the JC virus early transcription unit is differentially regulated by LCP-1 prior to but not after DNA replication, suggesting a novel mechanism by which DNA structure regulates eukaryotic gene expression.