The Xist (X inactive specific transcript) gene plays an essential role in X 
chromosome inactivation. To elucidate the mechanisms controlling Xist expression 
and X inactivation, we examined in vivo DNA-protein interactions in the Xist 
promoter region in a female mouse cell line (BMSL2), which has distinguishable 
Xist alleles. In vivo footprinting was accomplished by treatment of cells with 
dimethyl sulfate or ultraviolet light, followed by ligation-mediated polymerase 
chain reaction of purified DNA. The expressed allele on the inactive X 
chromosome and the silent allele on the active X chromosome were separated by 
the use of a restriction fragment length polymorphism prior to ligation-mediated 
polymerase chain reaction. The chromatin structure of the Xist promoter was 
found to be consistent with the activity state of the Xist gene. The silent 
allele (on the active X chromosome) showed no footprints, while the expressed 
allele (on the inactive X chromosome) showed footprints at a consensus sequence 
for a CCAAT box, two weak Sp1 sites, and a weak TATA box.