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Full-length mRNA sequencing reveals principles of poly(A) tail length control

ABSTRACT: Full-length mRNA sequencing reveals principles of poly(A) tail length control

PROVIDER: PRJNA522007 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8568880_subreads.fastq.gz	Fastqsanger.gz
	SRR8568871_subreads.fastq.gz	Fastqsanger.gz
	SRR8568881_subreads.fastq.gz	Fastqsanger.gz
	SRR8568872_subreads.fastq.gz	Fastqsanger.gz
	SRR8568882_subreads.fastq.gz	Fastqsanger.gz

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Full-length mRNA sequencing reveals principles of poly(A) tail length control

Project description:We report FLAM-seq, a cDNA library preparation method coupled to PacBio single-molecule sequencing for profiling full-length mRNAs including their poly(A) tail.

2019-06-04 | GSE126465 | GEO

Poly(A) tail length profiling of mRNAs from fission yeast

Project description:To obtain global data on polyadenylation of mRNAs, we fractionated the mRNAs according to their poly(A) tail length using a poly-U sepharose column followed by differential elution at five temperatures. Five mRNA fractions with distinct ranges of poly(A) tail length were then hybridized to microarrays using total eluate as a reference.

2007-05-16 | E-TABM-217 | biostudies-arrayexpress

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

Genome-wide measurement of LPS-induced Poly(A) tail length changes in macrophage cells

Project description:We applied Tail-end-displacement sequencing (TED-seq) for high-throughput profiling of poly(A) tail length dynamics induced by LPS stimulation in macrophage cells. We generate a time-course poly(A) tail length profiles in PMA-differentated THP-1 cells upon LPS stimulation (unstimulated, and post-stimulation 1, 2, and 4 h). This approach enabled us to profile induced poly(A) tail length dynamics with high accuracy and with 3´isoform resolution, generating a comprehensive view of poly(A) tail length dynamics induced upon an environmental signal in post-embryonic systems, and its biological implications.

2022-06-27 | GSE161188 | GEO

Poly(A) Tail Length of L4 C. elegans

Project description:Poly(A) Tail Length of L4 C. elegans

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Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos

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

Oppositional Poly(A) Tail Length Regulation by FMRP and CPEB1

Project description:Poly(A) tail length is regulated in both the nucleus and cytoplasm. One factor that controls polyadenylation in the cytoplasm is CPEB1, an RNA binding protein that associates with specific mRNA 3’UTR sequences to tether enzymes that add and remove poly(A). Two of these enzymes, the noncanonical poly(A) polymerases Gld2 (TENT2, PAPD4, Wispy) and Gld4 (TENT4B, PAPD5, TRF4, TUT3), interact with CPEB1 to extend poly(A). To identify additional RNA binding proteins that might anchor Gld4 to RNA, we expressed double tagged Gld4 in U87MG cells, which was used for sequential immunoprecipitation and elution followed by mass spectrometry. We identified several RNA binding proteins that co-precipitated with Gld4, among which was FMRP. To assess whether FMRP regulates polyadenylation, we performed TAIL-seq from WT and FMRP-deficient HEK293 cells. Surprisingly, loss of FMRP resulted in an overall increase in poly(A), which was also observed for several specific mRNAs. Conversely, loss of CPEB1 elicited an expected decrease in poly(A), which was examined in cultured neurons. We also examined polyadenylation in wild type (WT) and FMRP-deficient mouse brain cortex by direct RNA Nanopore™ sequencing, which identified RNAs with both increased and decreased poly(A). Our data show that FMRP has a role in mediating poly(A) tail length, which adds to its repertoire of RNA regulation.

2022-03-01 | GSE188840 | GEO

Poly(A)-capture full-length double-strand cDNA sequencing for transcriptome analysis

Project description:We tried two methods which are the DNase I treated full-length double-strand cDNA sequencing and the poly(A) capture full-length double-strand cDNA sequencing to avoid the non-specific genomic DNA amplification.

2022-06-29 | GSE192928 | GEO

The molecular basis of coupling between poly(A)-tail length and translational efficiency

Project description:In animal oocytes and early embryos, mRNA poly(A)-tail length strongly influences translational efficiency (TE), but later in development this coupling between tail length and TE disappears. Here, we elucidate how this coupling is first established and why it disappears. Overexpressing cytoplasmic poly(A)-binding protein (PABPC) in frog oocytes specifically improved translation of short-tailed mRNAs, thereby diminishing coupling between tail length and TE. Thus, coupling requires limiting PABPC, implying that in coupled systems longer-tail mRNAs better compete for limiting PABPC. In addition to expressing excess PABPC, post-embryonic cells had two other properties that prevented strong coupling: terminal-uridylation-dependent destabilization of mRNAs lacking bound PABPC, and a regulatory regime wherein PABPC contributes minimally to TE. Thus, these results revealed three fundamental mechanistic requirements for coupling and defined the context-dependent functions for PABPC, in which this protein promotes TE but not mRNA stability in coupled systems and mRNA stability but not TE in uncoupled systems.

2021-07-07 | GSE166544 | GEO

PAL-AI reveals genetic determinants that control poly(A)-tail length during oocyte maturation, with relevance to human infertility

Project description:In oocytes of mammals and other animals, gene regulation is mediated primarily through changes in poly(A)-tail length. Here, we introduce PAL-AI, an integrated neural network machine-learning model that accurately predicts tail-length changes in maturing oocytes of frogs and mammals. We show that PAL-AI learned known and previously unknown sequence elements and their contextual features that control poly(A)-tail length, enabling it to predict tail-length changes resulting from 3ʹ-UTR single-nucleotide substitutions. It also predicted tail-length-mediated translational changes, allowing us to nominate genes important for oocyte maturation. When comparing predicted tail-length changes in human oocytes with genomic datasets of the All of Us Research Program and gnomAD we found that genetic variants predicted to disrupt tail lengthening are under negative selection in the human population, thereby linking mRNA tail lengthening to human female fertility.

2025-06-26 | GSE280422 | GEO

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