The Fission Yeast RNA Binding Protein Mmi1 Regulates Meiotic Genes by Controlling Intron Specific Splicing and Polyadenylation Coupled RNA Turnover

Abstract

The polyA tails of mRNAs are monitored by the exosome as a quality control mechanism. We find that fission yeast, Schizosaccharomyces pombe, adopts this RNA quality control mechanism to regulate a group of 30 or more meiotic genes at the level of both splicing and RNA turnover. In vegetative cells the RNA binding protein Mmi1 binds to the primary transcripts of these genes. We find the novel motif U(U/C/G)AAAC highly over-represented in targets of Mmi1. Mmi1 can specifically regulate the splicing of particular introns in a transcript: it inhibits the splicing of introns that are in the vicinity of putative Mmi1 binding sites, while allowing the splicing of other introns that are far from such sites. In addition, binding of Mmi1, particularly near the 3' end, alters 3' processing to promote extremely long polyA tails of up to a kilobase. The hyperadenylated transcripts are then targeted for degradation by the nuclear exonuclease Rrp6. The nuclear polyA binding protein Pab2 assists this hyperadenylation-mediated RNA decay. Rrp6 also targets other hyperadenylated transcripts, which become hyperadenylated in an unknown, but Mmi1-independent way. Thus, hyperadenylation may be a general signal for RNA degradation. In addition, binding of Mmi1 can affect the efficiency of 3' cleavage. Inactivation of Mmi1 in meiosis allows meiotic expression, through splicing and RNA stabilization, of at least 29 target genes, which are apparently constitutively transcribed.

Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe

“…However, polyadenylation is well known to serve as a marker for degradation in bacteria (Steege 2000;Dreyfus and Régnier 2002) and plants (Lange et al 2009). Chen et al (2011) have further shown that the addition of an unusually long poly(A) tail ("hyperadenylation") to mRNA leads to degradation in S. pombe. Other cases of polyadenylation for RNA degradation are also known in S. cerevisiae (Kuai et al 2004).…”

“…An absent or short poly(A) tail can mark the transcript for degradation, as shown in bacteria and plants (Steege 2000;Dreyfus and Régnier 2002;Lange et al 2009;Chen et al 2011). Moreover, in higher eukaryotes alternative PAS can lead to production of longer or shorter transcript isoforms (Tian et al 2005).…”

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).…”

Relative contributions of the structural and catalytic roles of Rrp6 in exosomal degradation of individual mRNAs

“…Further studies on the mechanism of Mmi1-mediated RNA turnover showed the exosome degrades Mmi1-bound RNAs in vegetative cells, and is aided by polyadenylation of these RNAs (St-Andre et al 2010;Yamanaka et al 2010;Chen et al 2011). Previous studies have shown both rrp6 and dis3 mutations interfere with degradation of Mmi1 targets (Yamanaka et al 2010;Chen et al 2011). Some Mmi1 targets, such as rec8 mRNA, undergo Mmi1-dependent hyperadenylation and thus become a substrate for Rrp6.…”