Nuclear Factor Binding to a DNA Sequence Element That Represses MMTV Transcription Induces a Structural Transition and Leads to the Contact of Single-Stranded Binding Proteins with DNA

NRE1 is a DNA sequence element in the long terminal repeat of mouse mammary tumor virus through which viral transcription is repressed. In addition to double-stranded DNA binding, both upper- and lower-stranded NRE1 binding activities occur in nuclear extracts. All three binding activities appear to be important for transcriptional effects. We report that occupancy of NRE1 within linear double-stranded NRE1 induces a structural transition in upstream flanking DNA that is facilitated by Mg²⁺. This transition was reflected by the striking DNase I sensitivity of the DNA. As Mg²⁺ concentration was increased, discrete DNase I hypersensitivity on one face of the DNA progressed to complete degradation of template. On the DNA face opposite the DNase I hypersensitivity, Mg²⁺ promoted regularly spaced cleavage by the single-strand-specific cleavage agents KMnO₄ and S1 nuclease. Induction of degradation by DNase I occurred independently of MMTV sequences flanking NRE1, because nuclear extract-dependent DNase I sensitivity was conferred to an unrelated DNA fragment by introduction of a 23-bp NRE1-containing oligonucleotide. UV protein–DNA cross-linking revealed that addition of Mg²⁺ to a double-stranded NRE1 DNA binding assay induced conversion from a double- to a single-stranded protein–DNA cross-linking pattern. Thus, nuclear factor binding to NRE1 induces changes in DNA topology that promote the direct contact of single-stranded NREl binding factors with DNA.