Decoupling of degradation from deadenylation reshapes poly(A) tail length in yeast meiosis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA719131 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description: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.
2021-10-10 | GSE171329 | GEO
Project description:RNA tails play integral roles in the control of mRNA translation and decay. Guanylation of poly(A) tail was discovered recently, yet the enzymology and function remain obscure. Here we identify TUT3 (PAPD5) and TUT5 (PAPD7) (TUT3/5) as the enzymes responsible for mRNA guanylation. Purified TUT3/5 predominantly incorporate GTPs to generate a mixed poly(A) tail with intermittent non-adenosine residues. A single guanosine is sufficient to impede the deadenylation complex (CCR4-NOT) which trims the tail and exposes guanosine at the 3′ end. Consistently, the depletion of TUT3/5 leads to a decrease in mRNA half-life and abundance in cells. Thus, TUT3/5 produce a mixed tail which shields the mRNA from rapid deadenylation. Our study unveils the role of mixed tailing, and expands the complexity of post-transcriptional gene regulation.
2019-06-09 | GSE116349 | GEO
Project description:MicroRNA induces deadenylation of its targets according to the current model in the scientific community, but this model is based on the studies of a few individual genes. We tested the model by examining the global effect of miRNA on poly(A) tail of the targets. Synthetic miR-1 mimic was transfected into HeLa cells, and the poly(A) length was measured by TAIL-seq. Deadenylation of miR-1 targets was evident as early as 3 hours post-transfection without a significant change in mRNA level. After 6 or 9 hours, target mRNA level was substantially downregulated. Therefore, although there are some exceptions, our result confirms that, in general, miRNA indeed induces deadenylation. Furthermore, our kinetic global analysis confirms that deadenylation precedes mRNA decay. Four culture dishes of HeLa cells were treated with miR-1 all together, then collected and prepared for sequencing after different time of incubation (0, 3, 6, and 9 hours post-transfection)
2014-02-28 | E-GEOD-54114 | biostudies-arrayexpress
Project description:MicroRNA induces deadenylation of its targets according to the current model in the scientific community, but this model is based on the studies of a few individual genes. We tested the model by examining the global effect of miRNA on poly(A) tail of the targets. Synthetic miR-1 mimic was transfected into HeLa cells, and the poly(A) length was measured by TAIL-seq. Deadenylation of miR-1 targets was evident as early as 3 hours post-transfection without a significant change in mRNA level. After 6 or 9 hours, target mRNA level was substantially downregulated. Therefore, although there are some exceptions, our result confirms that, in general, miRNA indeed induces deadenylation. Furthermore, our kinetic global analysis confirms that deadenylation precedes mRNA decay.
2014-02-28 | GSE54114 | GEO
Project description:Poly(A) tails protect RNAs from degradation and deadenylation rates determine RNA stability. Deadenylation has mostly been investigated within the cytoplasm and the dynamics of poly(A) tail length after transcription are not well understood. Combining long-read sequencing with metabolic labeling and cell fractionations, we investigate deadenylation dynamics of newly synthesized poly(A) tails in vitro and in vivo. We report evidence for genome-wide synthesis of poly(A) tails longer than 200 nt which are enriched upon splicing inhibition. Metabolic labeling reveals rapid deadenylation of poly(A) tails within minutes after transcription. Fractionation experiments show that initial deadenylation is a nuclear process, and that different classes of transcripts, including long noncoding RNAs, have distinctive nuclear poly(A) tail lengths. Modelling deadenylation dynamics predicts that deadenylation in the nucleus is by an order of magnitude faster than in the cytoplasm. In summary, we suggest nuclear deadenylation as a novel regulatory layer which may determine stability and abundance before mRNAs reach the cytoplasm.
2023-01-07 | GSE188539 | GEO
Project description:During oocyte maturation and early embryonic development, poly(A)-tail lengths strongly influence mRNA translation. However, how tail lengths are controlled at different developmental stages has been unclear. Here, we performed tail-length and translational profiling of mRNA reporter libraries (each with > 10 million 3ʹ-UTR sequence variants) in frog oocytes and embryos, and fish embryos. These analyses revealed that the UUUUA motif specifies cytoplasmic polyadenylation and identified diverse context features that modulate the activity of this 5-mer. Additional sequence motifs drive stage-specific deadenylation in embryos, and UUUUA and C-rich motifs drive tail-length-independent translational repression in oocytes. A neural network model accurately predicts tail-length change during oocyte maturation in frogs, mice, and humans. Analyses of human sequence variants showed that those predicted to disrupt tail-length control have been under negative selection, implying that our insights into control of poly(A)-tail length and translation have implications for human health and fertility.
2024-02-15 | GSE241107 | GEO
Project description:Poly(A)-tail length and mRNA deadenylation play important roles in post-transcriptional gene regulation. Here, we report the regulation of mRNA expression, half-life, and polysome association in mouse embryonic stem cells by the Cnot3 subunit in the Ccr4-Not mRNA deadenylase complex.
2016-08-10 | GSE84953 | GEO
Project description:RNA tails play integral roles in the control of mRNA translation and decay. Guanylation of poly(A) tail was discovered recently, yet the enzymology and function remain obscure. Here we identify TUT3 (PAPD5) and TUT5 (PAPD7) (TUT3/5) as the enzymes responsible for mRNA guanylation. Purified TUT3/5 predominantly incorporate GTPs to generate a mixed poly(A) tail with intermittent non-adenosine residues. A single guanosine is sufficient to impede the deadenylation complex (CCR4-NOT) which trims the tail and exposes guanosine at the 3′ end. Consistently, the depletion of TUT3/5 leads to a decrease in mRNA half-life and abundance in cells. Thus, TUT3/5 produce a mixed tail which shields the mRNA from rapid deadenylation. Our study unveils the role of mixed tailing, and expands the complexity of post-transcriptional gene regulation.
2019-06-09 | GSE115529 | GEO
Project description:Mixed tailing by TUT3 and TUT5 shields mRNA from rapid deadenylation [TAIL-Seq]
| PRJNA478242 | ENA
Project description:RNA turnover in eukaryotes is triggered by decapping, believed to be activated mostly after deadenylation. To investigate simultaneous changes in RNA levels and poly(A) tail size we performed Nanopore RNA sequencing on total RNA extracted from S. cerevisiae strains in which the decapping enzyme Dcp2, or the deadenylation factors Ccr4 and Pop2 were depleted through an inducible degron system. Two fully independent replicate experiments were performed for wild type and the two mutant conditions.
2022-10-01 | GSE211782 | GEO