Role of non-coding antisense RNAs in epigenetic control of gene expression through RNAi independent mechanisms
Recent tiling array analyses show that eukaryotic genomes, including S. cerevisiae, are much more widely transcribed than expected and produce many intergenic or antisense non-coding RNAs, many of which are unstable and rapidly degraded by the nuclear exosome (Xu et al., 2009). Whether and how these non-coding RNAs participate in the regulation of gene expression is under intense investigation.
Small interfering (Si) RNAs have been implicated in transcriptional gene silencing (TGS) in S. pombe and higher eukaryotes. This process is unlikely to exist in S. cerevisiae, as this organism lacks all major components of the RNAi machinery. However, our work has revealed the existence in S. cerevisiae of alternate gene silencing mechanisms that depend on long non-coding RNAs. We have shown that loss of the exosome component Rrp6 results in PHO84 anti-sense RNA stabilization and repression of PHO84 sense transcription. Notably, anti-sense accumulation and PHO84 silencing also occur in chronologically aged cells, suggesting that Rrp6 activity is regulated in response to physiological changes. Importantly, the stabilization of PHO84 anti-sense RNAs is paralleled by the recruitment of the histone deacetylase Hda1 and deacetylation of the PHO84 promoter resulting in PHO84 gene silencing (Camblong et al., 2007, Figure 3). Our more recent data show that PHO84 anti-sense transcripts also induce TGS in trans, in a mechanism independent of Hda1. Thus, TGS in cis and trans operate through distinct pathways (Camblong et al., 2009).
Figure 3: Antisense stabilization during aging or following loss of Rrp6 is accompanied by Hda1 recruitment and histone deacetylation at the PHO84 promoter.
To address the generality of this regulation and decipher underlying mechanisms, our project aims at identifying other genes regulated like PHO84 using genome wide approaches, as well as developing genetic screens to identify factors involved in antisense production or mediating the effects of non-coding RNAs on chromatin both in cis and trans. Our studies on budding yeast may broaden our understanding of non-coding RNAs in gene regulation in higher eukaryotes, as similar RNAi-independent mechanisms probably exist in metazoa.