The mouse Xist gene is expressed exclusively from the inactive X chrom
osome and may control the initiation of X inactivation. We show that i
n somatic tissues the 5' end of the silent Xist allele on the active X
chromosome is fully methylated, while the expressed allele on the ina
ctive X is completely unmethylated. In tissues that undergo imprinted
paternal Xist expression and imprinted X inactivation, the paternal Xi
st allele is unmethylated, and the silent maternal allele is fully met
hylated. In the male germline, a developmentally regulated demethylati
on of Xist occurs at the onset of meiosis and is retained in mature sp
ermatozoa. This may be the cause of imprinted expression of the patern
al Xist allele. A role for methylation in the control of Xist expressi
on is further supported by the finding that in differentiating embryon
ic stem cells during the initiation of X inactivation, differential me
thylation of Xist alleles precedes the onset of Xist expression.