The Non-Coding Air RNA is Required for Silencing a Cluster of Autosomal Imprinted Genes

Denise Barlow
OAW Institute of Molecular Biology

In genomic imprinting one of the two parental alleles of an autosomal gene is epigenetically silenced by a cis-acting mechanism. A bidirectional silencer for a 400kb region that contains three imprinted maternally-expressed protein-coding genes (Igf2r, S1c22a2, S1c22a3), has previously been shown by targeted deletion to reside in a 3.7kb sequence that also contains the promoter for the imprinted paternally-expressed non-coding Air RNA. Air expression correlates with repression of all three genes on the paternal allele, however, the Air RNA overlaps just one of these genes in an antisense orientation. To test whether the Air RNA is indeed required for silencing, we have inserted a polyadenylation signal to truncate 96% of the RNA. The truncated Air allele maintains imprinted expression and methylation of the Air promoter but shows complete loss of silencing of the Igf2r/Slc22a2/Slc22a3 cluster on the paternal chromosome. These results indicate that non-coding RNAs can play an active role in genomic imprinting. Our results thus identify the existence of a novel RNA-dependent mechanism in genomic imprinting and also indicate the existence of mechanistic parallels between autosomal genomic imprinting and X chromosomal inactivation.