High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

Abstract

Meiosis is a complex developmental process that generates haploid cells from diploid progenitors. We measured messenger RNA (mRNA) abundance and protein production through the yeast meiotic sporulation program and found strong, stage-specific expression for most genes, achieved through control of both mRNA levels and translational efficiency. Monitoring of protein production timing revealed uncharacterized recombination factors and extensive organellar remodeling. Meiotic translation is also shifted toward noncanonical sites, including short open reading frames (ORFs) on unannnotated transcripts and upstream regions of known transcripts (uORFs). Ribosome occupancy at near-cognate uORFs was associated with more efficient ORF translation; in contrast, some AUG uORFs, often exposed by regulated 5′ leader extensions, acted competitively. This work reveals pervasive translational control in meiosis and helps to illuminate the molecular basis of the broad restructuring of meiotic cells.

Ndt80 activates the meiotic ORC1 transcript isoform and SMA2 via a bi-directional middle sporulation element in Saccharomyces cerevisiae

“…These findings agree with large-scale ribosome profiling data. 13 Our data suggest a novel role for the Ndt80 activator in yeast meiosis, which is to down-regulate Orc1 protein via induction of an untranslatable transcript isoform. The results therefore highlight an interesting regulatory design that enables an activator to repress a target gene product during eukaryotic cell differentiation.…”

“…1C). A Northern blot by Brar et al 2012 suggests that SK1 cells exclusively express the short ORC1 transcript isoform during vegetative growth and pre-meiotic DNA replication when Orc1 is needed. Critically, at the onset of meiotic M-phase approximately 6 hours after transfer into sporulation medium, cells completely switch to expressing the long transcript isoform.…”

“…Note that the meiotic isoform has the size predicted for a full-length ORC1 transcript with a 5 0 -extended UTR (see Fig. 5C in reference 13 ). Genomics data thus reveal a complex regulatory pattern involving 5 transcripts: haploid and diploid cells undergoing mitotic growth express SUT292 and divergent ORC1/XUT1538 transcripts downstream of it, while middle meiotic cells continue to express SUT292 but co-induce divergent mORC1/SMA2 transcripts via a developmentally regulated bi-directional promoter element (Fig.…”

“…8,10 The simplest explanation is that Sum1 contributes to the repression of mORC1 and SMA2 during mitotic growth, while Ndt80 activates the transcripts from middle meiosis onwards by directly interacting with a bi-directional MSE present in the ORC1 promoter. raises the interesting possibility that Ndt80 represses Orc1 after pre-meiotic DNA replication by activating a transcript isoform that sequesters ribosomes at its 5 0 end via uORFs; (reference 13 ; Fig. S3).…”

“…9,11,12 An earlier RNA-and ribosome profiling study of yeast sporulation reported that ORC1 encodes a meiotic isoform with an extended 5 0 -untranslated region (UTR) that was predicted to inhibit Orc1 translation during post-meiotic stages of spore development via upstream open reading frames (uORFs). 13 However, Orc1 protein levels during meiosis and gametogenesis have not been determined, and the transcription factors that control the expression of mORC1 during growth and development are unknown.…”