A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae

Abstract

Cryptic unstable transcripts (CUTs) are synthesized from intra-and intergenic regions in Saccharomyces cerevisiae and are rapidly degraded by RNA surveillance pathways, but their function(s) remain(s) elusive. Here, we show that an antisense TY1 CUT, starting within the Ty1 retrotransposon and encompassing the promoter 5 long terminal repeat (LTR), mediates RNA-dependent gene silencing and represses Ty1 mobility. We show that the Ty1 regulatory RNA is synthesized by RNA polymerase II, polyadenylated, and destabilized by the cytoplasmic 5 RNA degradation pathway. Moreover, the Ty1 regulatory RNA represses Ty1 transcription and transposition in trans by acting on the de novo transcribed TY1 RNA. Consistent with a transcriptional regulation mechanism, we show that RNA polymerase II occupancy is reduced on the Ty1 chromatin upon silencing, although TBP binding remains unchanged. Furthermore, the Ty1 silencing is partially mediated by histone deacetylation and requires Set1-dependent histone methylation, pointing out an analogy with heterochromatin gene silencing. Our results show the first example of an RNA-dependent gene trans-silencing mediated by epigenetic marks in S. cerevisiae. Recent data have shown that cryptic unstable transcripts (CUTs) are RNA polymerase II (RNAPII)-dependent noncoding RNAs (ncRNAs) corresponding to inter-and intragenic regions of the genome and may represent 10% of intergenic transcripts in Saccharomyces cerevisiae (Wyers et al. 2005). Under normal conditions, CUTs are almost undetectable, as they are rapidly degraded by the activity of Rrp6 and Trf4, members of the nuclear exosome and the TRAMP complex, respectively (LaCava et al. 2005;Vanacova et al. 2005;Wyers et al. 2005). In addition to Trf4 and Rrp6, the cytoplasmic 5Ј-3Ј exoribonuclease Xrn1 also plays an important role in the turnover of CUTs, supporting the idea that some of these transcripts escape the nuclear quality control and might have a cytoplasmic residency (Thompson and Parker 2007).Despite these observations, the function(s) of CUTs remain(s) poorly characterized. Cryptic transcription has been widely described from yeast to human and qualified as "transcriptional noise." Interestingly, it has been proposed that cryptic transcription allows RNA polymerase-dependent chromatin changes but not the production of functional RNA molecules, as those are immediately degraded (Struhl 2007). In agreement with this model, CUT transcription has been shown to interfere with promoters of coding regions and hence regulates gene expression in S. cerevisiae (Martens et al. 2005;Hongay et al. 2006;Uhler et al. 2007). However, alternative models emerged, providing a direct function for cryptic transcripts. Indeed, recent reports have shown that the processing of siRNAs in Schizosaccharomyces pombe is mediated by homologs of the TRAMP and exosome subunits (Buhler et al. 2007;Nicolas et al. 2007), strongly indicating that the fission yeast's siRNAs might originate from CUTs. It is tempting to hypothesize that CUTs in S. cerevisiae are link...

Divergent transcription: A new feature of active promoters

“…55,56 The generality of ncRNAs modulating transcription from promoters in their immediate vicinity is unknown, but these results suggest that DNA associated RNAs can be the targets of RNA binding proteins which interact with chromatin modifying enzymes and lead to changes in gene expression level.…”

T-body formation precedes virus-like particle maturation inS. cerevisiae

“…21,22 In addition, mutations resulting in C-terminal truncation of Gag an approach alternative to Gag-p49 induction, we examined the ability of tagTy1 to form T-bodies in the xrn1Δ strain. We chose this background due to the strong inhibition of Ty1 transposition in the absence of the Xrn1p exonuclease, 17 probably due to the accumulation of Ty1 antisense RNAs that inhibit VLP maturation. 17,18 Consistent with a previous report in reference 2, we observed significantly decreased T-body counts in xrn1Δ cells transformed with an empty vector (Fig.…”

“…We chose this background due to the strong inhibition of Ty1 transposition in the absence of the Xrn1p exonuclease, 17 probably due to the accumulation of Ty1 antisense RNAs that inhibit VLP maturation. 17,18 Consistent with a previous report in reference 2, we observed significantly decreased T-body counts in xrn1Δ cells transformed with an empty vector (Fig. 4).…”

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

“…Heterochromatic gene silencing has been most extensively described in Schizosaccharomyces pombe, where siRNAs originating from these regions target the RITS complex to induce repressive histone modifications (Volpe et al 2002; for review, see Buhler and Moazed 2007). Although, the complete RNAi machinery is absent in Saccharomyces cerevisiae (Aravind et al 2000), RNA-mediated TGS within euchromatin has been recently reported (Camblong et al 2007;Berretta et al 2008;Houseley et al 2008). In particular, we showed that stabilization of PHO84 antisense RNAs, escaping degradation by the nuclear exosome in the absence of the Rrp6 exoribonuclease or during chronological aging, leads to PHO84 TGS via a mechanism implicating the Hda1/2/3 histone deacetylase (Camblong et al 2007).…”