Sotta et al. 2022 (PRJNA594648)
General Details
| Title | Translational regulation in response to boron in Arabidopsis thaliana |
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| Organism | |
| Number of Samples | 6 |
| Release Date | 2019/12/10 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP235569 |
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| ENA | SRP235569 |
| GEO | GSE141765 |
| BioProject | PRJNA594648 |
Publication
| Title | |
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| Authors | Sotta N,Chiba Y,Miwa K,Takamatsu S,Tanaka M,Yamashita Y,Naito S,Fujiwara T |
| Journal | The Plant journal : for cell and molecular biology |
| Publication Date | 2021 Jun |
| Abstract | We previously reported that ribosome stalling at AUG-stop sequences in the 5'-untranslated region plays a critical role in regulating the expression of Arabidopsis thaliana NIP5;1, which encodes a boron uptake transporter, in response to boron conditions in media. This ribosome stalling is triggered specifically by boric acid, but the mechanisms are unknown. Although upstream open reading frames (uORFs) are known in many cases to regulate translation through peptides encoded by the uORF, AUG-stop stalling does not involve any peptide synthesis. The unique feature of AUG-stops - that termination follows immediately after initiation - suggests a possible effect of boron on the translational process itself. However, the generality of AUG-stop-mediated translational regulation and the effect of boron on translation at the genome scale are not clear. Here, we conducted a ribosome profiling analysis to reveal the genome-wide regulation of translation in response to boron conditions in A. thaliana shoots. We identified hundreds of translationally regulated genes that function in various biological processes. Under high-boron conditions, transcripts with reduced translation efficiency were rich in uORFs, highlighting the importance of uORF-mediated translational regulation. We found 673 uORFs that had more frequent ribosome association. Moreover, transcripts that were translationally downregulated under high-boron conditions were rich in minimum uORFs (AUG-stops), suggesting that AUG-stops play a global role in the boron response. Metagene analysis revealed that boron increased the ribosome occupancy of stop codons, indicating that this element is involved in global translational termination processes. © 2021 Society for Experimental Biology and John Wiley & Sons Ltd. |
| PMC | |
| PMID | 33772920 |
| 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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| SRR10620357 | PRJNA594648 | Arabidopsis thaliana | Ribo-Seq |  |
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| SRR10620358 | PRJNA594648 | Arabidopsis thaliana | Ribo-Seq | |
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| SRR10620359 | PRJNA594648 | Arabidopsis thaliana | Ribo-Seq | |
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| SRR10620360 | PRJNA594648 | Arabidopsis thaliana | Ribo-Seq | |
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| SRR10620361 | PRJNA594648 | Arabidopsis thaliana | Ribo-Seq | |
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| SRR10620362 | PRJNA594648 | Arabidopsis thaliana | 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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