The non-coding Air RNA is required for silencing autosomal imprinted genes

In genomic imprinting, one of the two parental alleles of an autosomal gene is silenced epigenetically by a cis-acting mechanism1, 2. A bidirectional silencer for a 400-kilobase region that contains three imprinted, maternally expressed protein-coding genes (Igf2r/Slc22a2/Slc22a3) has been shown by targeted deletion to be located in a sequence of 3.7 kilobases3, 4, 5, which also contains the promoter for the imprinted, paternally expressed non-coding Air RNA6. Expression of Air is correlated with repression of all three genes on the paternal allele5; however, Air RNA overlaps just one of these genes in an antisense orientation6. Here we show, by inserting a polyadenylation signal that truncates 96% of the RNA transcript, that Air RNA is required for silencing. The truncated Air allele maintains imprinted expression and methylation of the Air promoter, but shows complete loss of silencing of the Igf2r/Slc22a2/Slc22a3 gene cluster on the paternal chromosome. Our results indicate that non-coding RNAs have an active role in genomic imprinting.