Eisen et al. 2022 (PRJNA799348)
General Details
| Title | The Interplay Between Translational Efficiency, Poly(A) Tails, MicroRNAs, and Neuronal Activation |
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| Organism | |
| Number of Samples | 12 |
| Release Date | 2022/01/21 00:00 |
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| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP356162 |
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| ENA | SRP356162 |
| GEO | GSE194172 |
| BioProject | PRJNA799348 |
Publication
| Title | |
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| Authors | Eisen TJ,Li JJ,Bartel DP |
| Journal | RNA (New York, N.Y.) |
| Publication Date | 2022 Jun |
| Abstract | Neurons provide a rich setting for studying post-transcriptional control. Here, we investigate the landscape of translational control in neurons and search for mRNA features that explain differences in translational efficiency (TE), considering the interplay between TE, mRNA poly(A)-tail lengths, microRNAs, and neuronal activation. In neurons and brain tissues, TE correlates with tail length, and a few dozen mRNAs appear to undergo cytoplasmic polyadenylation upon light or chemical stimulation. However, the correlation between TE and tail length is modest, explaining <5% of TE variance, and even this modest relationship diminishes when accounting for other mRNA features. Thus, tail length appears to affect TE only minimally. Accordingly, miRNAs, which accelerate deadenylation of their mRNA targets, primarily influence target mRNA levels, with no detectable effect on either steady-state tail lengths or TE. Larger correlates with TE include codon composition and predicted mRNA folding energy. When combined in a model, the identified correlates explain 38%-45% of TE variance. These results provide a framework for considering the relative impact of factors that contribute to translational control in neurons. They indicate that when examined in bulk, translational control in neurons largely resembles that of other types of post-embryonic cells. Thus, detection of more specialized control might require analyses that can distinguish translation occurring in neuronal processes from that occurring in cell bodies. © 2022 Eisen et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society. |
| PMC | PMC9074895 |
| PMID | 35273099 |
| DOI |
| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) | ||
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| SRR17694825 | PRJNA799348 | Mus musculus | Ribo-Seq |  |
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| SRR17694824 | PRJNA799348 | Mus musculus | Ribo-Seq | |
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| SRR17694823 | PRJNA799348 | Mus musculus | Ribo-Seq | |
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| SRR17694819 | PRJNA799348 | Mus musculus | Ribo-Seq | |
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| SRR17694818 | PRJNA799348 | Mus musculus | Ribo-Seq | |
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| SRR17694817 | PRJNA799348 | Mus musculus | Ribo-Seq | |
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| SRR17694814 | PRJNA799348 | Mus musculus | Ribo-Seq | |
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| SRR17694813 | PRJNA799348 | Mus musculus | Ribo-Seq | |
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| SRR17694811 | PRJNA799348 | Mus musculus | Ribo-Seq | |
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| SRR17694807 | PRJNA799348 | Mus musculus | Ribo-Seq | |
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| SRR17694806 | PRJNA799348 | Mus musculus | Ribo-Seq | |
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| SRR17694805 | PRJNA799348 | Mus musculus | Ribo-Seq | |
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| Run Accession | Study Accession | Scientific Name | Cell Line | Library Type | Treatment | GWIPS-viz | Trips-Viz | Reads | BAM | BigWig (F) | BigWig (R) |
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