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| Status |
Public on May 15, 2023 |
| Title |
Mechanisms of stop codon readthrough mitigation reveal principles of GCN1 mediated translational quality control |
| Organisms |
Caenorhabditis elegans; Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Readthrough into the 3′ untranslated region (3′UTR) of the mRNA results in the production of aberrant proteins. Metazoans efficiently clear readthrough proteins, but the underlying mechanisms remain unknown. Here, we show in C. elegans and mammalian cells that readthrough proteins are targeted by a coupled, two-level quality control pathway involving the BAG6 chaperone complex and the ribosome collision-sensing protein GCN1. Readthrough proteins with hydrophobic C-terminal extensions are recognized by SGTA-BAG6 and ubiquitylated by RNF126 for proteasomal degradation. Additionally, cotranslational mRNA decay initiated by GCN1 and CCR4/NOT limits the accumulation of readthrough products. Unexpectedly, selective ribosome profiling uncovered a general role of GCN1 in regulating translation dynamics when ribosomes encounter nonoptimal codons, a feature of 3′UTR sequences. Dysfunction of GCN1 results in mRNA and proteome imbalance, increasingly perturbing transmembrane proteins and collagens during aging. These results define GCN1 as a key factor acting during translation in maintaining protein homeostasis.
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| Overall design |
Selective Ribo-seq of GCN1 in C.elegans and HEK293 with respective input controls and additional mRNAseq
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| Contributor(s) |
Mueller MB, Jayaraj GG, Hartl FU |
| Citation(s) |
37339632 |
| Submission date |
Sep 28, 2022 |
| Last update date |
Aug 14, 2023 |
| Contact name |
Martin Mueller |
| E-mail(s) |
mamueller@biochem.mpg.de
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| Organization name |
MPI of Biochemistry
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| Lab |
Hartl
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| Street address |
Am Klopferspitz 18
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| City |
Martinsried/Planegg |
| ZIP/Postal code |
82152 |
| Country |
Germany |
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| Platforms (4)
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| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL19757 |
Illumina NextSeq 500 (Caenorhabditis elegans) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL26672 |
Illumina NovaSeq 6000 (Caenorhabditis elegans) |
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| Samples (66)
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| GSM6605207 |
Input(Cele)_B, Ribo-seq |
| GSM6605208 |
GCN-1(nc40)_D0_A, Ribo-seq |
| GSM6605209 |
GCN-1(nc40)_D0_B, Ribo-seq |
| GSM6605210 |
Wild-type(N2)_D0_A, Ribo-seq |
| GSM6605211 |
Wild-type(N2)_D0_B, Ribo-seq |
| GSM6605212 |
GCN-1(nc40)_D6_A, Ribo-seq |
| GSM6605213 |
GCN-1(nc40)_D6_B, Ribo-seq |
| GSM6605214 |
Wild-type(N2)_D6_A, Ribo-seq |
| GSM6605215 |
Wild-type(N2)_D6_B, Ribo-seq |
| GSM6605216 |
YFP-STOP_A, Ribo-seq |
| GSM6605217 |
YFP-STOP_B, Ribo-seq |
| GSM6605218 |
YFP-UTR_A, Ribo-seq |
| GSM6605219 |
YFP-UTR_B, Ribo-seq |
| GSM6605220 |
Input_mRNA_A(Cele), RNA-seq |
| GSM6605221 |
Input_mRNA_B(Cele), RNA-seq |
| GSM6605222 |
YFP-STOP_mRNA_A, RNA-seq |
| GSM6605223 |
YFP-STOP_mRNA_B, RNA-seq |
| GSM6605224 |
YFP-UTR_mRNA_A, RNA-seq |
| GSM6605225 |
YFP-UTR_mRNA_B, RNA-seq |
| GSM6605226 |
GCN-1(nc40)_D0_A, RNA-seq |
| GSM6605227 |
GCN-1(nc40)_D0_B, RNA-seq |
| GSM6605228 |
Wild-type(N2)_D0_A, RNA-seq |
| GSM6605229 |
Wild-type(N2)_D0_B, RNA-seq |
| GSM6605230 |
GCN-1(nc40)_D6_A, RNA-seq |
| GSM6605231 |
GCN-1(nc40)_D6_B, RNA-seq |
| GSM6605232 |
Wild-type(N2)_D6_A, RNA-seq |
| GSM6605233 |
Wild-type(N2)_D6_B, RNA-seq |
| GSM6605234 |
GCN1-IP_Untreated(Hsap)_A, Ribo-seq |
| GSM6605235 |
GCN1-IP_Untreated(Hsap)_B, Ribo-seq |
| GSM6605236 |
GCN1-IP_CC885(Hsap)_A, Ribo-seq |
| GSM6605237 |
GCN1-IP_CC885(Hsap)_B, Ribo-seq |
| GSM6605238 |
Input_Untreated(Hsap)_A, Ribo-seq |
| GSM6605239 |
Input_Untreated(Hsap)_B, Ribo-seq |
| GSM6605240 |
Input_CC885(Hsap)_A, Ribo-seq |
| GSM6605241 |
Input_CC885(Hsap)_B, Ribo-seq |
| GSM6995331 |
GCN-1-IP(Cele)_A_disome |
| GSM6995332 |
GCN-1-IP(Cele)_B_disome |
| GSM6995333 |
Input(Cele)_A_disome |
| GSM6995334 |
Input(Cele)_B_disome |
| GSM6995335 |
WT_0h_A |
| GSM6995336 |
WT_0h_B |
| GSM6995337 |
WT_0h_C |
| GSM6995338 |
WT_2h_A |
| GSM6995339 |
WT_2h_B |
| GSM6995340 |
WT_2h_C |
| GSM6995341 |
WT_4h_A |
| GSM6995342 |
WT_4h_B |
| GSM6995343 |
WT_4h_C |
| GSM6995344 |
WT_8h_A |
| GSM6995345 |
WT_8h_B |
| GSM6995346 |
WT_8h_C |
| GSM6995347 |
GCN1_0h_A |
| GSM6995348 |
GCN1_0h_B |
| GSM6995349 |
GCN1_0h_C |
| GSM6995350 |
GCN1_2h_A |
| GSM6995351 |
GCN1_2h_B |
| GSM6995352 |
GCN1_2h_C |
| GSM6995353 |
GCN1_4h_A |
| GSM6995354 |
GCN1_4h_B |
| GSM6995355 |
GCN1_4h_C |
| GSM6995356 |
GCN1_8h_A |
| GSM6995357 |
GCN1_8h_B |
| GSM6995358 |
GCN1_8h_C |
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| Relations |
| BioProject |
PRJNA885130 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE214396_Counts_GCN1_IP_Cele.txt.gz |
289.4 Kb |
(ftp)(http) |
TXT |
| GSE214396_Counts_GCN1_IP_Cele_disome.txt.gz |
297.7 Kb |
(ftp)(http) |
TXT |
| GSE214396_Counts_GCN1_Total_mRNA.txt.gz |
213.0 Kb |
(ftp)(http) |
TXT |
| GSE214396_Counts_HEK293_CC885_ribo.txt.gz |
394.4 Kb |
(ftp)(http) |
TXT |
| GSE214396_Counts_HEK293_Untreated_ribo.txt.gz |
387.3 Kb |
(ftp)(http) |
TXT |
| GSE214396_Counts_NC40_aged_mRNA.txt.gz |
330.2 Kb |
(ftp)(http) |
TXT |
| GSE214396_Counts_NC40_aged_ribo.txt.gz |
316.1 Kb |
(ftp)(http) |
TXT |
| GSE214396_Counts_NC40_young_mRNA.txt.gz |
283.1 Kb |
(ftp)(http) |
TXT |
| GSE214396_Counts_NC40_young_ribo.txt.gz |
295.7 Kb |
(ftp)(http) |
TXT |
| GSE214396_Counts_YFP-UTR_mRNA.txt.gz |
287.3 Kb |
(ftp)(http) |
TXT |
| GSE214396_Counts_YFP-UTR_ribo.txt.gz |
229.0 Kb |
(ftp)(http) |
TXT |
| GSE214396_GCN1_halflives.csv.gz |
393.6 Kb |
(ftp)(http) |
CSV |
| GSE214396_WT_halflives.csv.gz |
393.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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