RNA Structure Coordinates Translation Across the Meiotic Program

Key results

1. 01

   ShownIn-cell DMS-MaP over nine stages (vegetative, pre-meiotic and seven synchronized meiotic stages) gave structures for most annotated yeast mRNAs; average structural complexity (Gini index) dropped at meiotic entry, stayed low to metaphase I and rose again at anaphase I.

   Pooled structures for 4,739 of 6,666 annotated mRNAs (median signal-to-noise 5.8; 3,399 with >80% coverage); stage-specific structures for 2,471 mRNAs, 2,084 spanning multiple stages; ∼180 million reads per stage; 350 read-depth threshold from replicate correlations. Mean Gini shifts: V-P P < 10^-44, P-T0 P < 10^-107, T2-T3 P < 10^-130. · High-resolution DMS-MaP Resolves mRNA Structures…; Figure legends

2. 02

   ShownTranscripts upregulated during meiosis (TUMs) are less structured than other mRNAs, and GC content or nucleotide composition does not explain the difference.

   1,078 TUMs from hierarchical clustering of 2,620 mRNAs changing ≥8-fold. Gini lower in TUMs (n = 937) than non-TUMs (n = 3,767), P < 10^-23; early vs late TUMs P = 0.061. ORF GC content did not differ (P = 0.4), and an adenosine-only Gini index still separated the groups. · Transcripts Upregulated During Meiosis Adopt…; Figure legends

3. 03

   ShownStructural complexity tracks lower translation efficiency (TE), more strongly in meiosis than vegetative growth. During meiosis (but not vegetative growth), Complex mRNAs show sharper ribosome flux drops at their most structured ORF window; Complex mRNAs also have more upstream ORF (uORF) translation.

   ORF Gini vs TE: Spearman r -0.35 to -0.56 at T1-T6 vs -0.21 to -0.36 at V-T0. Simple vs Complex TE: ∼1.4-fold in vegetative growth, >2.0-fold in meiosis. Flux drop after window 0: 1.4% group gap in vegetative growth vs ∼10% greater for Complex in meiosis; uORF translation twice as frequent in Complex. 390 transcripts with ≥4-fold TE change: GiniORF vs TE change r = -0.08, P = 0.16. · Coupled Preference for RNA Structure at…; Figure legends

4. 04

   ShownMore structured TUMs get ribosomes later (Simple-group share peaked at T3, 40%; Complex rose at T5, 8.7%, and T6, 20.5%). In CCW22, the most abundant meiotic mRNA, a long-range 5′UTR-3′UTR pairing holds back early translation; breaking it advances Ccw22p and delays meiosis.

   217 transcripts peaking in translation near meiotic exit were more structured than mid-meiosis ones; in region-level comparisons (UTRs with >20 A/C covered), late-translated mRNAs had more complex 5′UTRs (P = 0.016) and ORFs (P < 10^-9) but not 3′UTRs. CCW22 (Gini 0.414) uses a near-cognate AUA at -17 inside a 22 bp UTR-UTR stem; 3′UTR mutants advanced Ccw22p, compensatory 5′UTR mutants restored oscillation. · mRNA Structure Contributes to Stage-Specific…; Figure legends

5. 05

   ShownCytoplasmic RNA helicase expression runs high-low-high across meiosis. Raising Ded1p to near-vegetative levels during meiosis tilts protein output toward structured mRNAs, lowers TUM-encoded proteins, releases Ccw22p early and often arrests cells at or before metaphase II.

   Ded1p fell 50% from V to T0 (footprints and proteomics); CDC5-promoter DED1 brought it near vegetative level by T5. Proteomics: 149 up, 194 down (≥1.2-fold, P < 0.05); up genes had more complex mRNAs (P < 10^-5) and 5′UTRs (P = 0.014), down genes simpler ORFs (P < 10^-5). Gene set enrichment: TUM proteins fell, most for SPO19, SPR1, GAS4 (Gini 0.28, 0.27, 0.27). Arrest scored at 12 h post-induction. · mRNA Unwinding Power Oscillates to Coordinate…; Figure legends