Non-coding RNA and epigenetic silencing of gene expression

Air RNA and G9a association


Recent progress in high-throughput transcriptome analyses in mammals has revealed an unexpectedly large number of long non-coding RNAs (ncRNA) that do not encode proteins.

Most of these ncRNAs remain enigmatic, however some have attracted attention because they appear to be involved in epigenetic regulation of gene expression. The mechanisms by which large non-coding RNAs silence gene expression are unknown.


The Air ncRNA, appears to be required for placental silencing of three cis-linked genes Slc22a3, Slc22a2 and Igf2r, located within 400 kb from the Air transcription unit.

To investigate the possibility that Air is targeted to specific genomic regions, we used RNA TRAP (see above) and found marked accumulation of Air at the promoter region of the distal Slc22a3 gene.

Taking advantage of the developmental control of Air-dependent Slc22a3 repression, we showed that Air’s association with the Slc22a3 promoter correlated with Slc22a3 repression and repressive H3K9 histone methylation at the promoter.

These data reveal a specific interaction between the large ncRNA and promoter chromatin, rather than a uniform ‘coating’ mechanism throughout the entire gene cluster. Next we showed by RNA-IP that Air interacts with the histone methyltransferase G9a, which has been implicated in H3K9 methylation.

We showed that Air was required to target G9a to the Slc22a3 promoter to epigenetically silence gene expression. In addition, a critical role for G9a in silencing Slc22a3 was confirmed in G9a knockout mice.

​Taken together, this work provides answers for two important questions; where and how large ncRNAs work to achieve epigenetic regulation on chromatin. Our results suggest that Air recruits G9a to the Slc22a3 promoter to epigenetically silence gene expression.

However it is also possible that Air creates a repressive nuclear compartment that recruits G9a and the Slc22a3 promoter, to modify its chromatin structure and restrict its access to transcription factories (as has been suggested for Xist). This work reveals a potentially vast, previously unappreciated, regulatory network of large ncRNAs that play important roles in regulating gene expression.

For more information see: The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin (2008) Takashi Nagano, Jennifer A Mitchell, Lionel A Sanz, Florian M Pauler, Anne C Ferguson-Smith, Robert Feil & Peter Fraser
Science 322 (5908), 1717-1720