Repression of Meiotic Genes by Antisense Transcription and by Fkh2 Transcription Factor in Schizosaccharomyces pombe

Abstract

In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s) of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the “unspliced” signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression.

A dominant role for meiosis-specific 3′ RNA processing in controlling expression of a fission yeast cyclin gene

“…Whereas the signals and factors that positively regulate rem1 and other middle meiotic genes in fission yeast have been extensively investigated (Horie et al 1998;Abe and Shimoda 2000;Nakamura et al 2000;Watanabe et al 2001;Okuzaki et al 2003;Nakamura et al 2004;Malapeira et al 2005;Nakamura et al 2005;Ogino and Masai 2006;Mata et al 2007;Murakami-Tonami et al 2007;Moldon et al 2008;Nakase et al 2009), only three published reports have focused on negative regulation (Shimoseki and Shimoda 2001;Averbeck et al 2005;Chen et al 2012), and none of these examined polyadenylation. In the earliest, splicing of transcripts from the mes1 gene was shown to occur even in vegetative cells when a secondary structure in the 59 UTR was disrupted (Shimoseki and Shimoda 2001).…”

“…The most recent study reported that anti-sense transcripts that overlap many middle meiotic genes are present in vegetatively growing fission yeast cells (Chen et al 2012). These authors proposed that transcripts complementary to the mRNA were the source of signals attributed to unspliced RNA from middle meiotic genes in earlier studies (Averbeck et al 2005;Moldon et al 2008;Chen et al 2011).…”

“…Because the splicing assays employed here are strand-specific (see Materials and Methods for details), the proposed scenario does not apply. Why, then, were unspliced rem1 and spo4 RNAs not detected by Chen et al (2012) using a strand-specific assay? The apparent discrepancy is due to the fact that the anti-sense study was limited to poly(A) + RNA, whereas the unspliced rem1 and spo4 transcripts we detect here in proliferating and early meiotic cells are not properly cleaved and polyadenylated.…”

“…However, this may, at least in part, reflect analysis of total RNA here vs. poly(A) + RNA in the plant studies . Another potential parallel is that alternative polyadenylation in Arabidopsis is regulated by anti-sense transcripts (Hormyik et al 2010), as is middle meiotic gene expression in fission yeast (Chen et al 2012).…”

“…For early meiotic transcripts, prevention of RNA processing during proliferation is intimately linked to a specialized nuclear turnover mechanism that requires the RNA binding proteins Mmi1p and Red1p for targeting to the exosome (Harigaya et al 2006;McPheeters et al 2009;Yamanaka et al 2010;Chen et al 2011;Sugiyama and Sugioka-Sugiyama 2011). For middle meiotic genes, the forkhead transcription factor Fkh2p, expressed in both mitotic and meiotic cells, has been implicated in negative regulation, while a meiosis-specific member of this protein family, Mei4p, functions in positive control during meiosis (Malapeira et al 2005;Mata et al 2007;Moldon et al 2008;Chen et al 2012).…”