The influence of microRNAs and poly(A)-tail length on endogenous mRNA-protein complexes
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ABSTRACT:
PROVIDER: PRJNA381782 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5419610.fastq.gz | Fastqsanger.gz | |||
| SRR5419620.fastq.gz | Fastqsanger.gz | |||
| SRR5419630.fastq.gz | Fastqsanger.gz | |||
| SRR5419611.fastq.gz | Fastqsanger.gz | |||
| SRR5419621.fastq.gz | Fastqsanger.gz |
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Project description:All mRNAs are bound in vivo by proteins to form mRNA–protein complexes (mRNPs), but changes in the composition of mRNPs during post-transcriptional regulation remain largely unexplored. Here, we have analyzed, on a transcriptome-wide scale, how microRNA-mediated repression modulates the associations of core components (eIF4E, eIF4G, and PABP) and of the decay factor DDX6 in human cells. Despite the transient nature of repressed intermediates, we detected significant changes in mRNP composition, marked by dissociation of eIF4G and PABP, and by recruitment of DDX6. Furthermore, although poly(A)-tail length has been considered critical in post-transcriptional regulation, differences in steady-state tail length explained little of the variation in either PABP association or mRNP organization more generally. Instead, relative occupancy of core components correlated best with gene expression. Together, these results indicate that posttranscriptional regulatory factors influence the associations of PABP and other core factors, and do so without substantially affecting steady-state tail length.
2017-09-20 | GSE97438 | GEO
Project description:BackgroundAll mRNAs are bound in vivo by proteins to form mRNA-protein complexes (mRNPs), but changes in the composition of mRNPs during posttranscriptional regulation remain largely unexplored. Here, we have analyzed, on a transcriptome-wide scale, how microRNA-mediated repression modulates the associations of the core mRNP components eIF4E, eIF4G, and PABP and of the decay factor DDX6 in human cells.ResultsDespite the transient nature of repressed intermediates, we detect significant changes in mRNP composition, marked by dissociation of eIF4G and PABP, and by recruitment of DDX6. Furthermore, although poly(A)-tail length has been considered critical in post-transcriptional regulation, differences in steady-state tail length explain little of the variation in either PABP association or mRNP organization more generally. Instead, relative occupancy of core components correlates best with gene expression.ConclusionsThese results indicate that posttranscriptional regulatory factors, such as microRNAs, influence the associations of PABP and other core factors, and do so without substantially affecting steady-state tail length.
| S-EPMC5664449 | biostudies-literature
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
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
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
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
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
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
Project description:Poly(A) Tail Length of L4 C. elegans
| PRJNA412860 | ENA
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