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Series GSE183470 Query DataSets for GSE183470
Status Public on Sep 30, 2021
Title Controlling tissue patterning by translational regulation of signaling transcripts through the core translation factor eIF3c [I]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Although gene expression is tightly regulated during embryonic development, the impact of translational control has received less experimental attention. Here, we find that eukaryotic translation initiation factor-3 (eIF3) is required for Shh-mediated tissue patterning. Analysis of loss-of-function eIF3 subunit c (Eif3c) mice reveal a unique sensitivity to the Shh receptor Patched 1 (Ptch1) dosage. Genome-wide in vivo enhanced cross-linking immunoprecipitation sequence (eCLIP-seq) shows unexpected specificity for eIF3 binding to a pyrimidine rich motif present in subsets of 5’-UTRs and a corresponding change in the translation of these transcripts by ribosome profiling in Eif3c loss-of-function embryos. We further find that while Eif3c loss-of-function embryos do not show a global decrease in protein synthesis, translation of Ptch1 through this pyrimidine rich motif is specifically sensitive to eIF3 amount. Altogether, this work uncovers hidden specificity of housekeeping translation initiation machinery for the translation of key developmental signaling transcripts.
Overall design Ribosome profiling (Ribo-seq)/RNA-seq
Contributor(s) Fujii K, Zhulyn O, Byeon GW, Kerr C, Genuth N, Walsh E, Barna M
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Submission date Sep 05, 2021
Last update date Sep 30, 2021
Contact name Gun Woo Byeon
Organization name Stanford University
Street address 279 Campus Dr., Beckman Center B309
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (96)
GSM5558058 neural tube, Wild-type Ribo-seq (run2_TC1_WT_Ribo_S1_L004)
GSM5558059 neural tube, Wild-type Ribo-seq (run2_TC5_WT_Ribo_S2_L003)
GSM5558060 neural tube, Wild-type Ribo-seq (run2_TC6_WT_Ribo_S3_L002)
This SubSeries is part of SuperSeries:
GSE183472 Controlling tissue patterning by translational regulation of signaling transcripts through the core translation factor eIF3c
BioProject PRJNA760922
SRA SRP335745

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE183470_ribo_counts.txt.gz 23.6 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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