The steroid hormone vitamin D is a principal mediator of skeletal homeostasis. 1,25-Dihydroxyvitamin D3 treatment of ROS 17/2.8 osteoblast-like cells results in a ligand-dependent increase in transcription of the bone-specific osteocalcin gene. This transcriptional upregulation requires the positive cis-acting vitamin D responsive element (VDRE). We have used the ligation-mediated polymerase chain reaction to demonstrate that protein occupancy of the VDRE within the intact cell correlates with increased synthesis of osteocalcin transcripts. These protein-DNA contacts were not present in the absence of vitamin D or in osteosarcoma cells (ROS 24 Rodan (Merck Sharp & Dohme). Cells were maintained in F12 medium containing calcium and charcoal stripped 5% fetal calf serum for 5 days after plating before hormone treatment or vehicle control. 1,25(OH)2D3 was provided by Milan Uskokovic (Hoffman-La Roche).In Vivo Footprint Analysis. In vivo footprinting was performed by exposing cells to 0.1% dimethy sulfate (DMS) (Aldrich) in culture medium for 5 min at room temperature. Methylated genomic DNA was isolated and cleaved with piperidine (Sigma) (26), and the level of methylation protection of G residues was analyzed by the ligation-mediated single-sided polymerase chain reaction (LMPCR) footprinting technique (27). LMPCR was performed with Vent polymerase (New England Biolabs). First-strand synthesis was accomplished with primer 1 (5'-GACAAACTGGCTCCAAC-TCGCATAGC-3'; nt -358 to -383) in first-strand buffer [40 mM NaCl/10 mM Tris HCl, pH 8.9/4 mM MgSO4/0.01% nonacetylated bovine serum albumin (BSA) (New England Biolabs)/0.1% Triton X-100]. The DNA was ligated with the unidirectional linker primer (27). The DNA was amplified in amplification buffer (10 mM NaCl/20 mM Tris HCl, pH 8.9/2 mM MgSO4/0.01% nonacetylated BSA/0.1% Triton X-100) using primer 2 (5'-GCATAGCCTGTGATTTTCAGTGTCT-GCCGT-3'; nt -377 to -406) and the linker oligonucleotide. Eighteen cycles of PCR were performed, each involving denaturation at 96°C, annealing at 56°C, and elongation at 76°C as described (27). Labeling was performed with 32p-end-labeled primer 3 (5'-AGCCTGTGATTTTCAGTGTCTAbbreviations: 1,25(OH)2D3, 1,25-dihydroxyvitamin D3; VDR, vitamin D receptor; VDRE, vitamin D responsive element; DMS, dimethyl sulfate; LMPCR, ligation-mediated single-sided PCR.