Das et al. 2019 (PRJNA464051)
General Details
Title | Widespread Alterations in Translation Elongation in the Brain of Fmr1 Knock-Out Mice |
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Organism | |
Number of Samples | 14 |
Release Date | 2018/05/04 00:00 |
Sequencing Types | |
Protocol Details |
Study Links
GWIPS-viz | Trips-Viz |
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Visit Trips-Viz |
Repository Details
SRA | SRP144655 |
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ENA | SRP144655 |
GEO | GSE114064 |
BioProject | PRJNA464051 |
Publication
Title | |
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Authors | Das Sharma S,Metz JB,Li H,Hobson BD,Hornstein N,Sulzer D,Tang G,Sims PA |
Journal | Cell reports |
Publication Date | 2019 Mar 19 |
Abstract | FMRP (fragile X mental retardation protein) is a polysome-associated RNA-binding protein encoded by Fmr1 that is lost in fragile X syndrome. Increasing evidence suggests that FMRP regulates both translation initiation and elongation, but the gene specificity of these effects is unclear. To elucidate the impact of Fmr1 loss on translation, we utilize ribosome profiling for genome-wide measurements of ribosomal occupancy and positioning in the cortex of 24-day-old Fmr1 knockout mice. We find a remarkably coherent reduction in ribosome footprint abundance per mRNA for previously identified, high-affinity mRNA binding partners of FMRP and an increase for terminal oligopyrimidine (TOP) motif-containing genes canonically controlled by mammalian target of rapamycin-eIF4E-binding protein-eIF4E binding protein-eukaryotic initiation factor 4E (mTOR-4E-BP-eIF4E) signaling. Amino acid motif- and gene-level analyses both show a widespread reduction of translational pausing in Fmr1 knockout mice. Our findings are consistent with a model of FMRP-mediated regulation of both translation initiation through eIF4E and elongation that is disrupted in fragile X syndrome. Copyright © 2019 The Author(s). Published by Elsevier Inc. All rights reserved. |
PMC | PMC6457272 |
PMID | 30893603 |
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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SRR7124015 | PRJNA464051 | Mus musculus | RNA-Seq | ||||||||||
SRR7124016 | PRJNA464051 | Mus musculus | RNA-Seq | ||||||||||
SRR7124017 | PRJNA464051 | Mus musculus | RNA-Seq | ||||||||||
SRR7124018 | PRJNA464051 | Mus musculus | RNA-Seq | ||||||||||
SRR7124019 | PRJNA464051 | Mus musculus | RNA-Seq | ||||||||||
SRR7124020 | PRJNA464051 | Mus musculus | RNA-Seq | ||||||||||
SRR7124021 | PRJNA464051 | Mus musculus | RNA-Seq | ||||||||||
SRR7124022 | PRJNA464051 | Mus musculus | RNA-Seq | ||||||||||
SRR7124023 | PRJNA464051 | Mus musculus | Ribo-Seq | ||||||||||
SRR7124024 | PRJNA464051 | Mus musculus | Ribo-Seq | ||||||||||
SRR7124025 | PRJNA464051 | Mus musculus | Ribo-Seq | ||||||||||
SRR7124026 | PRJNA464051 | Mus musculus | Ribo-Seq | ||||||||||
SRR7124027 | PRJNA464051 | Mus musculus | Ribo-Seq | ||||||||||
SRR7124028 | PRJNA464051 | Mus musculus | Ribo-Seq | ||||||||||
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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