Fragile X syndrome is caused by silencing of the fragile X mental retardation 1 gene (FMR1) and consequent loss of its associated protein product. Silencing of FMR1 was known to correlate with the presence of trinucleotide repeats adjacent to the FMR1 promoter. Colak et al. now demonstrate that FMR1 silencing is due to direct binding of the trinucleotide repeat region of FMR1 mRNA to the FMR1 promoter DNA. Formation of such DNA–mRNA duplexes may represent a general mechanism of epigenetic silencing in nucleotide repeat disorders.