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Short Poly(A) Tails are a Conserved Feature of Highly Expressed Genes

ABSTRACT: Short Poly(A) Tails are a Conserved Feature of Highly Expressed Genes

PROVIDER: PRJNA412858 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6125151.fastq.gz	Fastqsanger.gz
	SRR6125152.fastq.gz	Fastqsanger.gz
	SRR6125153.fastq.gz	Fastqsanger.gz
	SRR6125154.fastq.gz	Fastqsanger.gz
	SRR6125155_1.fastq.gz	Fastqsanger.gz

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Short Poly(A) Tails are a Conserved Feature of Highly Expressed Genes

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-10-19 | GSE104502 | GEO

Short poly(A) tails are a conserved feature of highly expressed genes.

Project description:Poly(A) tails are important elements in mRNA translation and stability, although recent genome-wide studies have concluded that poly(A) tail length is generally not associated with translational efficiency in nonembryonic cells. To investigate whether poly(A) tail size might be coupled to gene expression in an intact organism, we used an adapted TAIL-seq protocol to measure poly(A) tails in Caenorhabditis elegans. Surprisingly, we found that well-expressed transcripts contain relatively short, well-defined tails. This attribute appears to be dependent on translational efficiency, as transcripts enriched for optimal codons and ribosome association had the shortest tail sizes, whereas noncoding RNAs retained long tails. Across eukaryotes, short tails were a feature of abundant and well-translated mRNAs. This seems to contradict the dogma that deadenylation induces translational inhibition and mRNA decay and suggests that well-expressed mRNAs accumulate with pruned tails that accommodate a minimal number of poly(A)-binding proteins, which may be ideal for protective and translational functions.

| S-EPMC5877826 | biostudies-literature

Comprehensive analysis of Poly(A) tails in Mouse Testes and Ovaries using Nanopore direct RNA Sequencing. 

Project description:Germ cell development, gametogenesis, is a complex process in which dysfunction leads to infertility, a growing health and sociological problem worldwide. In both spermatogenesis and oogenesis, post-transcriptional gene expression regulation is crucial. Essentially, all mRNAs possess non-templated poly(A) tails, which composition and dynamics (elongation, shortening, and modifications) determine the fate of mRNA. In this context, we present a comprehensive transcriptomic dataset that focuses on mRNA poly(A) tails metabolism in murine testes. Analyzed RNA samples are isolated from wild-type and transgenic mice lacking TENT5C polymerase, which can extend poly(A) tails in the cytoplasm. Both whole testes material, as well as male gametes at different developmental stages (round or long spermatids) were analyzed.

2024-09-10 | GSE273264 | GEO

URT1-mediated uridylation shapes poly(A) tails in Arabidopsis

Project description:URT1-mediated uridylation shapes poly(A) tails in Arabidopsis

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The Interplay Between Translational Efficiency, Poly(A) Tails, MicroRNAs, and Neuronal Activation

Project description:The Interplay Between Translational Efficiency, Poly(A) Tails, MicroRNAs, and Neuronal Activation

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Poly(A) Tail Length of L4 C. elegans

Project description:Poly(A) tails are important elements in mRNA translation and stability. However, recent genome-wide studies concluded that poly(A) tail length was generally not associated with translational efficiency in non-embryonic cells. To investigate if poly(A) tail size might be coupled to gene expression in an intact organism, we used an adapted TAIL-seq protocol to measure poly(A) tails in Caenorhabditis elegans. Surprisingly, we found that well-expressed transcripts contain relatively short, well-defined tails. This attribute appears dependent on translational efficiency, as transcripts enriched for optimal codons and ribosome association had the shortest tail sizes, while non-coding RNAs retained long tails.

2017-10-19 | GSE104501 | GEO

Poly(A)-tail profiling reveals an embryonic switch in translational control

Project description:Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater understanding of poly(A)-tail function. Here we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts, cell lines, Arabidopsis thaliana leaves, mouse liver, and zebrafish and frog embryos. Poly(A)-tail lengths were conserved between orthologous mRNAs, with mRNAs encoding ribosomal proteins and other 'housekeeping' proteins tending to have shorter tails. As expected, tail lengths were coupled to translational efficiencies in early zebrafish and frog embryos. However, this strong coupling diminished at gastrulation and was absent in non-embryonic samples, indicating a rapid developmental switch in the nature of translational control. This switch complements an earlier switch to zygotic transcriptional control and explains why the predominant effect of microRNA mediated deadenylation concurrently shifts from translational repression to mRNA destabilization. 64 samples from a variety of species

2014-01-29 | E-GEOD-52809 | biostudies-arrayexpress

Translation of poly(A) tails leads to precise mRNA cleavage and widespread ribosome rescue

Project description:Translation of poly(A) tails leads to mRNA cleavage but the mechanism and global pervasiveness of this “nonstop/no-go” decay process is not understood. Here we performed ribosome profiling of short 15-18 nt mRNA footprints to identify ribosomes stalled at 3’ ends of mRNA decay intermediates. We found mRNA cleavage extending hundreds of nucleotides upstream of ribosome stalling in poly(A) and predominantly in one reading frame. These observations suggest that cleavage is closely associated with the ribosome. Surprisingly, ribosomes appeared to stall when as few as 3 consecutive ORF-internal lysine codons were positioned in the A, P, and E sites though significant mRNA degradation was not observed. Endonucleolytic cleavage was widespread, however, at sites of premature polyadenylation and rescue of the ribosomes stalled at these sites was dependent on Dom34. These results suggest this process may be critical when changes in polyadenylation occur during development, tumorigenesis, or when translation termination/recycling is impaired.

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Poly(A)-tail profiling reveals an embryonic switch in translational control

2014-01-29 | GSE52809 | GEO

Determination of MHV RNA poly(A) tail length and 3' end additions upon NCTC cells infection

Project description:The mouse hepatitis virus (MHV) genomic and sub-genomic RNAs have 3’ poly(A) tails. The terminal addition of uridines to poly(A) tails has been shown to be a widespread modification. Here, we investigated the presence of 3' end additions on the MHV RNA poly(A) tails. To this end, we infected NCTC cells with MHV and isolated RNA at 24-hours post-infection (hpi). While the median poly(A) tail length of the MHV RNAs is around 50 nucleotides, we observed a peak of uridylation in transcripts with poly(A) tails about 40 nucleotides long

2023-03-23 | GSE200414 | GEO

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