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Mixed tailing by TUT3 and TUT5 shields mRNA from rapid deadenylation [TAIL-Seq]

ABSTRACT: 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.

ORGANISM(S): Homo sapiens Drosophila melanogaster

PROVIDER: GSE116349 | GEO | 2019/06/09

REPOSITORIES: GEO

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Mixed tailing by TUT3 and TUT5 shields mRNA from rapid deadenylation [RNA-Seq]

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

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

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

An extended wave of global mRNA deadenylation sets up a switch in translation regulation across the mammalian oocyte-to-embryo transition

Project description:The oocyte-to-embryo transition (OET) occurs in the absence of new transcription and relies on post-transcriptional gene regulation, including translational control by mRNA poly(A) tail regulation, where cytoplasmic polyadenylation activates translation and deadenylation leads to translational repression and decay. However, how the transcriptome-wide landscape of mRNA poly(A) tails shapes translation across the OET in mammals remains unknown. Here, we performed long-read RNA sequencing to uncover poly(A) tail lengths and mRNA abundance transcriptome-wide in mice across five stages of development from oocyte to embryo. Integrating these data with recently published ribosome profiling data, we demonstrate that poly(A) tail length is coupled to translational efficiency across the entire OET. We uncover an extended wave of global deadenylation during fertilization, which sets up a switch in translation control between the oocyte and embryo. In the oocyte, short-tailed maternal mRNAs that resist deadenylation in the oocyte are translationally activated, whereas large groups of mRNAs deadenylated without decay in the oocyte are later readenylated to drive translation activation in the early embryo. Our findings provide an important resource and insight into the mechanisms by which cytoplasmic polyadenylation and deadenylation dynamically shape poly(A) tail length in a stage-specific manner to orchestrate development from oocyte to embryo in mammals.

2024-03-14 | GSE228001 | GEO

Poly(A) tail length change of miRNA targets in HeLa cells

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

The 3′ extremity of mRNA unveiled by TAIL-seq

Project description:Global investigation of the 3′ extremity of mRNA, despite its importance in gene regulation, has not been feasible due to technical challenges associated with homopolymeric sequences and relative paucity of mRNA. By developing a new methodology, TAIL-seq, we find a number of unforeseen features at the 3′ termini of mRNA. Our analyses reveal the transcriptome-wide distribution of poly(A) tail and estimate the median poly(A) length as 55-60 nt in mammalian cells, which is substantially shorter than generally conceived. Poly(A) length correlates with mRNA half-life but not with translation efficiency. Surprisingly, we find widespread uridylation and guanylation at the downstream of poly(A) tail. The U-tails are generally attached to short poly(A) tails (<25 nt) while the G-tails are found mainly on longer poly(A) tails (>40 nt), implicating their generic roles in mRNA stability control. In addition, TAIL-seq identifies, with a single nucleotide resolution, numerous nucleolytic events involved in microRNA processing and mRNA cleavage.

2014-02-28 | GSE51299 | GEO

Determination of MHV virion genome poly(A) tail length and 3' end additions.

Project description:The mouse hepatitis virus (MHV) genomic RNA has a poly(A) tail required for replication. Here we investigated the presence of terminal poly(A) tail uridylation and guanylation in the virion RNA. After isolating the viral RNA followed by sequencing, we found a mean poly(A) tail of 66 nucleotides long with a peak of terminal uridylation on tails 55 to 66 nucleotides long.

2023-03-23 | GSE200415 | GEO

The 3′ extremity of mRNA unveiled by TAIL-seq

2014-02-28 | E-GEOD-51299 | biostudies-arrayexpress

Poly(A) tail length change of miRNA targets in HeLa cells

2014-02-28 | E-GEOD-54114 | biostudies-arrayexpress

Rapid nuclear deadenylation of mammalian messenger RNA

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

Cnot3-dependent mRNA deadenylation safeguards the pluripotent state

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

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