Negative Regulation of Meiotic Gene Expression by the Nuclear Poly(a)-binding Protein in Fission Yeast

Abstract

Meiosis is a cellular differentiation process in which hundreds of genes are temporally induced. Because the expression of meiotic genes during mitosis is detrimental to proliferation, meiotic genes must be negatively regulated in the mitotic cell cycle. Yet, little is known about mechanisms used by mitotic cells to repress meiosis-specific genes. Here we show that the poly(A)-binding protein Pab2, the fission yeast homolog of mammalian PABPN1, controls the expression of several meiotic transcripts during mitotic division. Our results from chromatin immunoprecipitation and promoter-swapping experiments indicate that Pab2 controls meiotic genes post-transcriptionally. Consistently, we show that the nuclear exosome complex cooperates with Pab2 in the negative regulation of meiotic genes. We also found that Pab2 plays a role in the RNA decay pathway orchestrated by Mmi1, a previously described factor that functions in the post-transcriptional elimination of meiotic transcripts. Our results support a model in which Mmi1 selectively targets meiotic transcripts for degradation via Pab2 and the exosome. Our findings have therefore uncovered a mode of gene regulation whereby a poly(A)-binding protein promotes RNA degradation in the nucleus to prevent untimely expression.Meiosis is a key differentiation process essential for the generation of genetically distinct individuals. During yeast meiosis, two cells of opposite mating types fuse and conjugate their DNA to form a diploid cell. This diploid cell undergoes DNA replication followed by two rounds of cell division to produce four haploid cells. Although many of the activities used to achieve cell division are common to both meiosis and mitosis, there are several features unique to meiosis. Importantly, the meiotic and mitotic cell cycles are mutually exclusive, and genes required for meiotic differentiation are solely expressed during meiosis. Such negative control of meiotic genes during mitosis suggests important regulatory systems to avoid inappropriate activation of meiosis. To date, however, the molecular mechanisms by which meiotic differentiation genes are suppressed during the mitotic cell cycle remain poorly understood.In the fission yeast Schizosaccharomyces pombe, meiotic differentiation involves the temporal activation of hundreds of genes (1). Although previous studies have established the importance of transcriptional regulation during fission yeast meiosis (1, 2), recent results implicate post-transcriptional mechanisms of gene regulation, including pre-mRNA splicing and mRNA degradation. Accordingly, several meiotic genes are specifically spliced during meiosis, but remain unspliced during the mitotic cell cycle (3, 4). Selective mRNA turnover is another mechanism used by fission yeast to ensure the absence of meiosis-specific transcripts during the mitotic cell cycle. The rapid elimination of specific meiotic transcripts in mitotic cells requires the YTH-family RNA-binding protein, Mmi1 (5). Mmi1 promotes the destruction of specific meiotic transcripts...

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6

“…The protein is thus predominantly required for efficient 5.8S rRNA 3′-end formation and mitotic processing of snRNAs, snoRNAs, and ncRNAs, the latter in cooperation with Pap2 (9,16,20,40,45). Importantly, fission yeast Rrp6 was recently shown to target meiotic mRNAs untimely expressed during mitotic growth and the meiotic ncRNA encoded by the sme2 gene, which is essential for Meiosis I (13,46,47). This is in keeping with the finding that Rrp6 targets MUTs and other meiotically induced ncRNAs during vegetative growth in the distantly related yeast S. cerevisiae.…”

“…Moreover, the exosome, which includes the RNase D-type exoribonuclease Rrp6 involved in mitotic ncRNA turnover, is conserved from yeasts to mammals (8)(9)(10)(11). Importantly, the fission yeast ortholog of Rrp6 was shown to be involved not only in the mitotic degradation of meiotic mRNAs but also of at least one meiotic noncoding transcript encoded by sme2 (12,13).…”

Conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing

“…Given the functional connection between 3′-end processing and degradation factors (18)(19)(20)(21), we asked whether the elimination factors Mmi1 and Rrp6 are required for premature termination of DSR-containing gene transcripts. Remarkably, the loss of Mmi1 or Rrp6 prevented premature termination of ssm4 and mcp5 transcripts upstream of the DSR (Fig.…”

“…Meiotic mRNAs that contain a determinant of selective removal (DSR) are recognized by the sequence-specific RNA-binding protein Mmi1 (16). Mmi1 in turn recruits MTREC and the Pir1/Iss10 protein to promote exosome-mediated elimination of transcripts and to recruit the Clr4 methyltransferase for heterochromatin island assembly (11,13,15,(17)(18)(19)(20). MTREC also localizes to regions of the genome that do not assemble heterochromatin, suggesting that additional factors are needed to direct the formation of heterochromatin islands (11).…”

Analysis of RNA Metabolism in Fission Yeast

“…Another key development was the demonstration that this process is regulated (McPheeters et al 2009;Yamanaka et al 2010), at least in part by a poly(A) binding protein present in mammals and fission yeast but absent in budding yeast (St-André et al 2010). To date, mechanistic studies have been scant beyond the early demonstration by the Proudfoot laboratory that mutating either cis-acting signals or trans-acting factors leads to readthrough transcription resulting from coupling between transcription termination and processing by the cleavage and polyadenylation machinery (Birse et al 1997;Aranda and Proudfoot 2001).…”