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Methylation of CpG sequences in and around CGG triplet repeats in FMR1 gene has strong correlation with manifestation of the fragile X syndrome in human patients. In contrast, we have observed a lack of correlation between repeat instability and DNA methylation in three different transgenic mouse models harboring unstable CGG repeats. Further we have demonstrated that the endogenous copy of mouse Fmr1 gene remains unmethylated both in males and females. These results imply that methylation and repeat instability are independent events and raise the possibility that methylation could also result in repression of FMR1 transcription in the absence of repeat expansion.