Decoupling of degradation from deadenylation reshapes poly(A) tail length in yeast meiosis

Nascent mRNA is endowed with a poly(A) tail, which is subject to gradual deadenylation in the cytoplasm, followed by mRNA degradation. Deadenylation and degradation rates are typically correlated, rendering it difficult to dissect the individual determinants governing each of these processes. In addition, the mechanistic basis for the coupling between deadenylation and degradation and the extent to which the two can be decoupled are largely unknown. Here we developed an approach allowing systematic, robust and multiplexed quantification of poly(A) tails. Our results suggest that in yeast, exclusively during meiosis, mRNA deadenylation and degradation rates are decoupled. The decoupled regime in meiosis allowed us to discover transcript length as a major determinant of deadenylation rates and as a key  contributor to the reshaping of poly(A) tail lengths in meiosis. The meiosis-specific decoupling also led to unique positive associations between poly(A) tail length and gene expression. The decoupling of degradation from deadenylation is also strongly associated with a focal localization pattern of the RNA degradation factor Xrn1 and can be phenocopied by deletion of Xrn1 under non-meiotic conditions. Importantly, the association of transcript length with deadenylation rates is conserved across eukaryotes. This study uncovers a new factor that shapes deadenylation rate and discovers a unique context in which degradation is decoupled from deadenylation. Exp1: After induction of meiosis RNA was extracted at 1hr interval timepoints for 9Hrs. Exp2: Yeast cells after 1 and 7 Hrs in SPO were transferred to YPD and RNA was extracted after 5 and 20min incubation. Exp3:In Wt, ccr4Δ/Δ, pop2Δ/Δ, and xrn1Δ/Δ strains RNA was extracted in vegetative growth, premeiotic conditions and after 5Hrs in SPO. Exp4: RNA was extracted in control cells and degron-Xrn1 cells growing in YPD2% before and after degradation of Xrn1. Exp5: RNA was extracted in control cells and pCup1-Ccr4 cells growing in YPD2% before and after induction of Ccr4. For all experiments poly(A) tail length was quantified using mPAT-seq and gene expression using RNA-seq.