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

Abstract

Meiotic gene regulation provides a rich source of insight into mechanisms of temporal control during development. We previously reported that accumulation of many meiotic mRNAs in fission yeast is governed by changes in 39 RNA processing and elucidated the molecular basis of this regulatory mechanism for an early meiotic gene. Here, we report that cleavage/polyadenylation is also the nexus of negative control for middle meiotic genes. Parallel profiles of splicing and polyadenylation are observed over a meiotic time course for both rem1 and spo4 but not for a constitutive control gene. Nevertheless, polyadenylation of rem1 transcripts is restricted to meiosis by a splicing-independent mechanism. Through systematic sequence substitutions, we identified a negative control region (NCR) located upstream of the rem1 transcription start site and found that it is required to block 39 RNA processing in proliferating cells. Ablation of the NCR relieves inhibition regardless of whether the intron is present, absent, or carries splice site mutations. Consistent with the previous report of a polypeptide encoded by the first exon of rem1, we discovered a second 39 processing site just downstream from the 59 splice site. Polyadenylation within the intron is activated concurrent with the downstream site during meiosis, is controlled by the NCR, and is enhanced when splicing is blocked via 59 junction or branch point mutations. Taken together, these data suggest a novel regulatory mechanism in which a 59 element modulates the dynamic interplay between splicing and polyadenylation.

Fungal Pre-mRNA 3′-End Processing

“…A subset of meiotic genes in S. pombe was also shown to undergo APA upon meiosis induction, and it was suggested to be important for the regulation of their expression (McPheeters et al 2009;Cremona et al 2011;Potter et al 2012). The mechanisms involved are discussed in a following paragraph.…”

“…Even though the ratio between the short and the long isoforms slightly changes during the time course of meiosis, the distal PAS is always more predominantly used over the proximal PAS (McPheeters et al 2009;Chen et al 2011). Later studies identified additional meiotic transcripts using meiosis specific 3 0 processingdependent regulation (Cremona et al 2011;Potter et al 2012). These transcripts were found to utilize more than one PAS upon meiosis induction, but again in this case the proximal PAS usage relatively to the distal PAS was not studied in detail.…”

DSIF factor Spt5 coordinates transcription, maturation and exoribonucleolysis of RNA polymerase II transcripts

“…We demonstrate that in the absence of the Integrator complex, Spt5 plays a central role in restricting non-coding transcription, possibly representing an ancient mechanism to control transcription within the non-coding genome. Therefore, we propose that Spt5/4 plays a role in restricting transcriptional output from promoters of lowly expressed genes such as non-coding genes that are also supressed by the post-transcriptional mechanisms 109,112,[131][132][133][134] .…”