Kraushar et al. 2021 (PRJNA661275)
General Details
| Title | Ribosome profiling analysis of Neuro2a cells with Ebp1 knockdown |
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| Organism | |
| Number of Samples | 6 |
| Release Date | 2020/09/03 00:00 |
| Sequencing Types | |
| Protocol Details |
Study Links
| GWIPS-viz | Trips-Viz |
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Repository Details
| SRA | SRP279969 |
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| ENA | SRP279969 |
| GEO | GSE157423 |
| BioProject | PRJNA661275 |
Publication
| Title | |
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| Authors | Kraushar ML,Krupp F,Harnett D,Turko P,Ambrozkiewicz MC,Sprink T,Imami K,Günnigmann M,Zinnall U,Vieira-Vieira CH,Schaub T,Münster-Wandowski A,Bürger J,Borisova E,Yamamoto H,Rasin MR,Ohler U,Beule D,Mielke T,Tarabykin V,Landthaler M,Kramer G,Vida I,Selbach M,Spahn CMT |
| Journal | Molecular cell |
| Publication Date | 2021 Jan 21 |
| Abstract | Protein synthesis must be finely tuned in the developing nervous system as the final essential step of gene expression. This study investigates the architecture of ribosomes from the neocortex during neurogenesis, revealing Ebp1 as a high-occupancy 60S peptide tunnel exit (TE) factor during protein synthesis at near-atomic resolution by cryoelectron microscopy (cryo-EM). Ribosome profiling demonstrated Ebp1-60S binding is highest during start codon initiation and N-terminal peptide elongation, regulating ribosome occupancy of these codons. Membrane-targeting domains emerging from the 60S tunnel, which recruit SRP/Sec61 to the shared binding site, displace Ebp1. Ebp1 is particularly abundant in the early-born neural stem cell (NSC) lineage and regulates neuronal morphology. Ebp1 especially impacts the synthesis of membrane-targeted cell adhesion molecules (CAMs), measured by pulsed stable isotope labeling by amino acids in cell culture (pSILAC)/bioorthogonal noncanonical amino acid tagging (BONCAT) mass spectrometry (MS). Therefore, Ebp1 is a central component of protein synthesis, and the ribosome TE is a focal point of gene expression control in the molecular specification of neuronal morphology during development. Copyright © 2020 Elsevier Inc. All rights reserved. |
| PMC | PMC8163098 |
| PMID | 33357414 |
| 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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| SRR12581851 | PRJNA661275 | Mus musculus | Neuro2a | Ribo-Seq |  |
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| SRR12581852 | PRJNA661275 | Mus musculus | Neuro2a | Ribo-Seq | |
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| SRR12581853 | PRJNA661275 | Mus musculus | Neuro2a | Ribo-Seq | |
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| SRR12581854 | PRJNA661275 | Mus musculus | Neuro2a | Ribo-Seq | |
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| SRR12581855 | PRJNA661275 | Mus musculus | Neuro2a | Ribo-Seq | |
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| SRR12581856 | PRJNA661275 | Mus musculus | Neuro2a | 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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