Eukaryotic initiation factor EIF-3.G augments mRNA translation efficiency to regulate neuronal activity
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, United States
Figures
Figure 1 with 3 supplements
eif-3.G(C130Y) suppresses acr-2(gf) convulsion behavior in the cholinergic motor neurons.
(A) Illustration of the genomic locus of eif-3.G: Peif-3.G denotes the promoter, blue boxes are exons for coding sequences and gray for 3′UTR. Arrowhead indicates guanine to adenine change in ju807; …
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Figure 1—source data 1
Source data for Figure 1C.
Quantification of convulsions per 60 s in strains of the indicated genotypes.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig1-data1-v2.xlsx
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Figure 1—source data 2
Source data for Figure 1E.
Quantification of convulsions per 60 s in the indicated strains.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig1-data2-v2.xlsx
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Figure 1—source data 3
Source data for Figure 1F.
Quantification of convulsions per 60 s in strains. Strain name or genotype is indicated in top row.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig1-data3-v2.xlsx
Figure 1—figure supplement 1
EIF-3.G is highly conserved and expressed ubiquitously.
(A) Clustal-W sequence alignment of C. elegans EIF-3.G (NP_001263666.1) with the S. cerevisiae (TIF-35; 32% identity; NP_010717.1) and human (eIF3g, 35% identity; AAC78728.1) orthologs. Residues …
Figure 1—figure supplement 2
Motor neuron development is normal in eif-3.G(C130Y) animals.
(A) Representative confocal z-stack projection images of axonal commissures projecting from motor neurons of wild type or eif-3.G(C130Y) single mutant L4 animals (head to the right). The …
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Figure 1—figure supplement 2—source data 1
Source data for Figure 1—figure supplement 2A.
Quantification of axonal commissures in strains of the indicated genotypes.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig1-figsupp2-data1-v2.xlsx
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Figure 1—figure supplement 2—source data 2
Source data for Figure 1—figure supplement 2B.
Quantification of synaptic puncta in strains of the indicated genotypes.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig1-figsupp2-data2-v2.xlsx
Figure 1—figure supplement 3
EIF-3.G(C130Y) modulation of convulsion behavior does not involve reduced EIF-3 complex dosage or ACR-2 expression.
(A) Quantification of convulsion frequencies in animals of the indicated genotypes; the corresponding strains (left to right) are: MT6241, CZ27434, CZ27435, CZ21759, CZ27433, CZ27436. Error bars are …
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Figure 1—figure supplement 3—source data 1
Source data for Figure 1—figure supplement 3A.
Quantification of convulsions per 60 s in strains of the indicated genotypes.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig1-figsupp3-data1-v2.xlsx
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Figure 1—figure supplement 3—source data 2
Source data for Figure 1—figure supplement 3B.
Quantification of relative fluorescence intensity in the indicated strains.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig1-figsupp3-data2-v2.xlsx
Figure 2
eif-3.G(C130Y) involves a selective function of EIF-3.G on translational control.
(A) Quantification of convulsion frequency in animals expressing GFP::EIF-3.G(WT) or GFP::EIF-3.G(C130Y) under Peif-3.G in the indicated genetic backgrounds; and the strains (left to right) are: …
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Figure 2—source data 1
Source data for Figure 2A.
Quantification of convulsions per 60 s in the indicated strains.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig2-data1-v2.xlsx
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Figure 2—source data 2
Source data for Figure 2B.
Quantification of relative fluorescence intensity in the indicated strains.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig2-data2-v2.xlsx
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Figure 2—source data 3
Source data for Figure 2C.
Quantification of polysome to monosome ratios in wildtype(N2) and strains of the indicated genotypes.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig2-data3-v2.xlsx
Figure 3
eif-3.G(C130Y) requires the RNA-binding domain (RRM) to suppress acr-2(gf) behaviors.
Top illustration of the EIF-3.G protein showing the EIF-3.I binding region (blue), zinc finger (ZF), RRM (dark grey), Q191* mutation in the EIF-3.G(∆RRM) transgene, RNP motifs (purple), and the RFF …
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Figure 3—source data 1
Source data for Figure 3.
Quantification of convulsions per 60 s in the indicated strains.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig3-data1-v2.xlsx
Figure 4 with 2 supplements
Both EIF-3.G(WT) and EIF-3.G(C130Y) associate with mRNA 5′UTRs in the cholinergic motor neurons.
(A) Pie charts displaying the proportion of EIF-3.G(WT) and EIF-3.G(C130Y) footprints located within each gene feature. (B) seCLIP read density track of EIF-3.G(WT) and EIF-3.G(C130Y) footprints on …
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Figure 4—source data 1
Source data for Figure 4A.
Number of read clusters representing footprints of EIF-3.G(WT) or EIF-3.G(C130Y) mapping to 5′UTR proximal or 3′UTR regions.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig4-data1-v2.xlsx
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Figure 4—source data 2
Source data for Figure 4C.
seCLIP reads for EIF-3.G(WT) and EIF-3.G(C130Y) 5’UTR proximal footprints represented as log2(reads per million).
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig4-data2-v2.xlsx
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Figure 4—source data 3
Source data for Figure 4D.
Cumulative EIF-3.G(WT) and EIF-3.G(C130Y) footprint coverage per base distance from the start codon (5’UTR proximal footprints) or stop codon (3’UTR footprints) represented as reads per million.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig4-data3-v2.xlsx
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Figure 4—source data 4
Source data for Figure 4E.
Length of 5’UTRs in mRNAs expressed in the ACh-MN transcriptome and EIF-3.G targets.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig4-data4-v2.xlsx
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Figure 4—source data 5
Source data for Figure 4F.
Percent GC of 5’UTRs in mRNAs expressed in the ACh-MN transcriptome and EIF-3.G targets.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig4-data5-v2.xlsx
Figure 4—figure supplement 1
EIF-3.G transgenes are expressed and produce similar results from replicate seCLIP experiments.
(A) Western blotting from strains expressing each indicated 3xFLAG-tagged EIF-3.G transgene in the ACh-MNs under the Punc-17β promoter. Quantification of expression intensity relative to the actin …
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Figure 4—figure supplement 1—source data 1
Source data for Figure 4—figure supplement 1A.
Quantification of band intensities from western blots using the indicated antibodies in each strain.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig4-figsupp1-data1-v2.xlsx
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Figure 4—figure supplement 1—source data 2
Source data for Figure 4—figure supplement 1B.
Number of EIF-3.G(WT), EIF-3.G(C130Y), or EIF-3.G(∆RRM) seCLIP reads mapping to each indicated gene.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig4-figsupp1-data2-v2.xlsx
Figure 4—figure supplement 2
EIF-3.G associates with long and GC-rich 5′UTRs.
(A) Pie charts show the proportion of trans-splicing (ts) among genes with 5′UTR proximal EIF-3.G footprints according to Allen et al. Unannotated genes were absent from the Allen et al. dataset. (B)…
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Figure 4—figure supplement 2—source data 1
Source data for Figure 4—figure supplement 2A.
Number of EIF-3.G target genes exhibiting trans-splicing.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig4-figsupp2-data1-v2.xlsx
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Figure 4—figure supplement 2—source data 2
Source data for Figure 4—figure supplement 2B.
Length of 5’UTRs among trans-spliced or non-trans-spliced mRNAs expressed in the C. elegans transcriptome or EIF-3.G target mRNAs.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig4-figsupp2-data2-v2.xlsx
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Figure 4—figure supplement 2—source data 3
Source data for Figure 4—figure supplement 2C.
Percent GC in 10nt bins up to 150nt from the start codon for each indicated gene.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig4-figsupp2-data3-v2.xlsx
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Figure 4—figure supplement 2—source data 4
Source data for Figure 4—figure supplement 2D.
Length of 5’UTRs among mRNAs expressed in the human(hg38) transcriptome or human eIF3 target mRNAs.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig4-figsupp2-data4-v2.xlsx
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Figure 4—figure supplement 2—source data 5
Source data for Figure 4—figure supplement 2E.
Percent GC in 5’UTRs among mRNAs expressed in the human(hg38) transcriptome or human eIF3 target mRNAs.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig4-figsupp2-data5-v2.xlsx
Figure 5
Gene network analyses of EIF-3.G target mRNAs show enrichment in activity-dependent expression.
(A) Cytoscape network of EIF-3.G target genes with enriched GO terms (neuropeptide signaling, response to stress, and protein translation and protein metabolism) or KEGG pathways (calcium and …
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Figure 5—source data 1
Source data for Figure 5B.
Foldchange in transcript expression in the cholinergic neuronal transcriptome of acr-2(gf) and wild-type animals.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig5-data1-v2.xlsx
Figure 6 with 1 supplement
EIF-3.G(C130Y) impairs HLH-30 expression in ACh-MNs of acr-2(gf) animals.
(A) Gene models of hlh-30 isoforms a (pink), b (blue), and d (green), with presumptive promoters for each isoform depicted as right-pointing arrows and the 5′UTR of isoform d in green to the right …
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Figure 6—source data 1
Source data for Figure 6C.
Quantification of relative fluorescence intensity in strains of the indicated genotypes.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig6-data1-v2.xlsx
Figure 6—figure supplement 1
EIF-3.G (C130Y) has no effect on translation of hlh-30.a in the ACh-MNs.
Representative single-plane confocal images of hlh-30a isoform-specific reporter (sqIs17, with the expression construct illustrated above) in ACh-MNs in animals of the indicated genotypes. Scale bar …
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Figure 6—figure supplement 1—source data 1
Source data for Figure 6—figure supplement 1.
Quantification of relative fluorescence intensity in strains of the indicated genotypes.
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Figure 7 with 1 supplement
Regulation of NCS-2 expression by EIF-3.G depends on its GC-rich 5′UTR.
(A) Illustration of the ncs-2 genomic region. Dark blue represents 5′UTR, green boxes are coding exons, and gray is the 3′UTR. The inset below shows the read density track of seCLIP footprints on …
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Figure 7—source data 1
Source data for Figure 7B.
Quantification of relative fluorescence intensity in strains of the indicated genotypes.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig7-data1-v2.xlsx
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Figure 7—source data 2
Source data for Figure 7C.
Quantification of relative fluorescence intensity in the indicated strains.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig7-data2-v2.xlsx
Figure 7—figure supplement 1
EIF-3.G(C130Y) reduces NCS-2 expression in the ACh-MNs of acr-2(gf) animals dependent on its conserved 5′UTR.
(A) Plot shows conservation of nucleotides (by phyloP135way scores) in the 5′UTR sequences of ncs-2 (blue) and eif-3.G (red), with higher scores indicating greater conservation. Genomic position …
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Figure 7—figure supplement 1—source data 1
Quantification of relative fluorescence intensity in the indicated strains.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig7-figsupp1-data1-v2.xlsx
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Figure 7—figure supplement 1—source data 2
Quantification of relative fluorescence intensity in the indicated strains.
- https://cdn.elifesciences.org/articles/68336/elife-68336-fig7-figsupp1-data2-v2.xlsx
Videos
Video 1
N2 [Wild type] C. elegans movement on solid nematode growth media.
Video 2
MT6241 [acr-2(gf)] C. elegans movement on solid nematode growth media.
Video 3
CZ21759 [eif-3.G(C130Y); acr-2(gf)] C. elegans movement on solid nematode growth media.
Video 4
CZ22197 [eif-3.G(C130Y)] C. elegans movement on solid nematode growth media.
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Antibody | anti-FLAG (Rabbit) | Sigma-Aldrich | Cat# F7425, RRID:AB_439687 | WB (1:2000) |
| Antibody | anti-Actin clone C4 (Mouse monoclonal) | MP Biomedicals | Cat# 08691002, RRID:AB_2335304 | WB (1:2000) |
| Antibody | Anti-FLAG M2 Magnetic Beads | Sigma-Aldrich | Cat# M8823, RRID:AB_2637089 | IP |
| Recombinant protein reagent | Cas9-NLS (purified protein) | UC Berkely QB3 | ||
| Genetic reagent (C. elegans) | + | CGC | RRID:CGC_N2 | |
| Genetic reagent (C. elegans) | acr-2(n2420) X | Jospin et al., 2009 | MT6241 | |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II | This work | CZ22197 | Figure 1F |
| Genetic reagent (C. elegans) | eif-3.G(ju1840) II | This work | CZ28494 | Figure 1C |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X | This work | CZ21759 | Figure 1C |
| Genetic reagent (C. elegans) | eif-3.G(ju1840) II; acr-2(n2420) X | This work | CZ28495 | Figure 1C |
| Genetic reagent (C. elegans) | eif-3.G(ju1327) / mnC1 II | This work | CZ22974 | Figure 1F |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx7015 | This work | CZ22976 | Figure 1C |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx7016 | This work | CZ22977 | Figure 1C |
| Genetic reagent (C. elegans) | eif-3.G(ju807) I;acr-2(n2420) X; juEx7045 | This work | CZ23125 | Figure 1E |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X; juEx7046 | This work | CZ23126 | Figure 1E |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X; juEx7019 | This work | CZ22980 | Figure 1E |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X; juEx7020 | This work | CZ22981 | Figure 1E |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X; juEx7439 | This work | CZ23791 | Figure 1E |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X; juEx7440 | This work | CZ23880 | Figure 1E |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X; juEx7021 | This work | CZ22982 | Figure 1E |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X; juEx7022 | This work | CZ22983 | Figure 1E |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X; juEx8062 | This work | CZ27881 | Figure 1E |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X; juEx8063 | This work | CZ27882 | Figure 1E |
| Genetic reagent (C. elegans) | eif-3.G(ju1327) /mnC1 II; acr-2(n2420) X | This work | CZ23310 | Figure 1F |
| Genetic reagent (C. elegans) | eif-3.G(ju807) / eif-3.G(ju1327) II | This work | CZ25714 | Figure 1F |
| Genetic reagent (C. elegans) | eif-3.G(ju807) / eif-3.G(ju1327) II; acr-2(n2420) X | This work | CZ26828 | Figure 1F |
| Genetic reagent (C. elegans) | juSi320 IV | This work | CZ24063 | Figure 2B; Figure 1—figure supplement 1B |
| Genetic reagent (C. elegans) | eif-3.G(ju1327) /mnC1 II; juSi320 IV | This work | CZ24079 | Figure 2A |
| Genetic reagent (C. elegans) | juSi320 IV; acr-2(n2420) X | This work | CZ24729 | Figure 2A |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; juSi320 IV; acr-2(n2420) X | This work | CZ28107 | Figure 2A |
| Genetic reagent (C. elegans) | juSi331 IV | This work | CZ24651 | Figure 2B; Figure 1—figure supplement 1B |
| Genetic reagent (C. elegans) | juSi331 IV; acr-2(n2420) X | This work | CZ24652 | Figure 2A |
| Genetic reagent (C. elegans) | eif-3.G(ju1327) / mnC1 II; juSi331 IV; acr-2(n2420) X | This work | CZ28497 | Figure 2A |
| Genetic reagent (C. elegans) | juIs14 IV | Wang et al., 2017 | CZ631 | |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; juIs14 IV | This work | CZ24161 | Figure 1—figure supplement 2 |
| Genetic reagent (C. elegans) | juIs14 IV; acr-2(n2420) X | McCulloch et al., 2020 | CZ5808 | |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; juIs14 IV; acr-2(n2420) X | This work | CZ8905 | Figure 1—figure supplement 2A |
| Genetic reagent (C. elegans) | nuIs94 | Hallam et al., 2000 | KP2229 | |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; nuIs94 | This work | CZ24021 | Figure 1—figure supplement 2B |
| Genetic reagent (C. elegans) | acr-2(n2420) X; nuIs94 | This work | CZ5815 | Figure 1—figure supplement 2B |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420)X; nuIs94 | This work | CZ24021 | Figure 1—figure supplement 2B |
| Genetic reagent (C. elegans) | eif-3.E(ok2607) I / hT2 I,III; acr-2(n2420) X | This work | CZ27434 | Figure 1—figure supplement 3A |
| Genetic reagent (C. elegans) | eif-3.E(ok2607) I / hT2 I, III; eif-3.G(ju807) II; acr-2(n2420) X | This work | CZ27433 | Figure 1—figure supplement 3A |
| Genetic reagent (C. elegans) | eif-3.H(ok1353) I / hT2 I, III; acr-2(n2420) X | This work | CZ27435 | Figure 1—figure supplement 3A |
| Genetic reagent (C. elegans) | eif-3.H(ok1353) I / hT2 I, III; eif-3.G(ju807) II; acr-2(n2420) X | This work | CZ27436 | Figure 1—figure supplement 3A |
| Genetic reagent (C. elegans) | oxSi39 IV | Qi et al., 2013 | CZ12338 | |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; oxSi39 IV | This work | CZ23854 | Figure 1—figure supplement 3B |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx7056 | This work | CZ23203 | Figure 3 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx7057 | This work | CZ23204 | Figure 3 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx8100 | This work | CZ28152 | Figure 3 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx8101 | This work | CZ28153 | Figure 3 |
| Genetic reagent (C. elegans) | juEx7113 | This work | CZ26777 | Figure 3 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx7114 | This work | CZ23304 | Figure 3 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx7115 | This work | CZ23305 | Figure 3 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx8095 | This work | CZ28066 | Figure 3 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx8096 | This work | CZ28067 | Figure 3 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx8087 | This work | CZ28057 | Figure 3 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx8088 | This work | CZ28058 | Figure 3 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx8089 | This work | CZ28064 | Figure 3 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx8090 | This work | CZ28065 | Figure 3 |
| Genetic reagent (C. elegans) | unc-119(tm4063) III; wgIs433 | Sarov et al., 2006 | OP433 | |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; unc-119(tm4063)III; wgIs433 | This work | CZ28145 | Figure 6C |
| Genetic reagent (C. elegans) | acr-2(n2420) X; unc-119(tm4063) III; wgIs433 | This work | CZ27913 | Figure 6C |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; unc-119(tm4063) III; acr-2(n2420) X; wgIs433 | This work | CZ27914 | Figure 6C |
| Genetic reagent (C. elegans) | sqIs17 | Dittman and Kaplan, 2006 | MAH240 | |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; sqIs17 | This work | CZ28334 | Figure 6—figure supplement 1 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; sqIs17 | This work | CZ28212 | Figure 6—figure supplement 1 |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X; sqIs17 | This work | CZ28218 | Figure 6—figure supplement 1 |
| Genetic reagent (C. elegans) | unc-13(s69) I; wgIs433 | This work | CZ28491 | Figure 6C |
| Genetic reagent (C. elegans) | unc-13(s69) I; acr-2(n2420) X; wgIs433 | This work | CZ28492 | Figure 6C |
| Genetic reagent (C. elegans) | unc-13(s69) I; eif-3.G(ju807); acr-2(n2420) X; wgIs433 | This work | CZ28493 | Figure 6C |
| Genetic reagent (C. elegans) | juSi260 ncs-2(tm1943) I | Zhou et al., 2017 | CZ22459 | |
| Genetic reagent (C. elegans) | juSi260 ncs-2(tm1943) I; eif-3.G(ju807) II | This work | CZ23225 | Figure 7B |
| Genetic reagent (C. elegans) | juSi260 ncs-2(tm1943) I; acr-2(n2420) X | This work | CZ22345 | Figure 7B |
| Genetic reagent (C. elegans) | juSi260 ncs-2(tm1943) I; eif-3.G(ju807) II; acr-2(n2420) X | This work | CZ28110 | Figure 7B |
| Genetic reagent (C. elegans) | juSi391 ncs-2(tm1943) I | This work | CZ28213 | Figure 7C |
| Genetic reagent (C. elegans) | juSi391 ncs-2(tm1943) I; eif-3.G(ju807) II | This work | CZ28340 | Figure 7C |
| Genetic reagent (C. elegans) | juSi391 ncs-2(tm1943) I;acr-2(n2420) X | This work | CZ28252 | Figure 7C |
| Genetic reagent (C. elegans) | juSi391 ncs-2(tm1943) I;eif-3.G(ju807) II; acr-2(n2420) X | This work | CZ28253 | Figure 7C |
| Genetic reagent (C. elegans) | juSi392 ncs-2(tm1943) I | This work | CZ28277 | Figure 7—figure supplement 1B |
| Genetic reagent (C. elegans) | juSi392 ncs-2(tm1943) I;eif-3.G(ju807) II | This work | CZ28312 | Figure 7—figure supplement 1B |
| Genetic reagent (C. elegans) | juSi392 ncs-2(tm1943) I; acr-2(n2420) X | This work | CZ28291 | Figure 7—figure supplement 1B |
| Genetic reagent (C. elegans) | juSi392 ncs-2(tm1943) I; eif-3.G(ju807) II; acr-2(n2420) X | This work | CZ28292 | Figure 7—figure supplement 1B |
| Genetic reagent (C. elegans) | juSi393 ncs-2(tm1943) I | This work | CZ28278 | Figure 7—figure supplement 1C |
| Genetic reagent (C. elegans) | juSi393 ncs-2(tm1943) I; eif-3.G(ju807) II | This work | CZ28311 | Figure 7—figure supplement 1C |
| Genetic reagent (C. elegans) | juSi393 ncs-2(tm1943) I; acr-2(n2420) X | This work | CZ28293 | Figure 7—figure supplement 1C |
| Genetic reagent (C. elegans) | juSi393 ncs-2(tm1943) I; eif-3.G(ju807) II; acr-2(n2420) X | This work | CZ28294 | Figure 7—figure supplement 1C |
| Genetic reagent (C. elegans) | juEx2045 | --- | CZ9635 | |
| Genetic reagent (C. elegans) | hlh-30(tm1978) IV | CGC | CZ23321 | |
| Genetic reagent (C. elegans) | hlh-30(tm1978) IV; acr-2(n2420) X | This work | CZ28174 | Related to Figure 6C |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; hlh-30(tm1978) IV; acr-2(n2420) X | This work | CZ28175 | Related to Figure 6C |
| Genetic reagent (C. elegans) | eif-3.G(ju1327) II /mnC1; juSi363 IV; acr-2(n2420) X | This work | CZ26759 | Related to Figure 4—figure supplement 1A |
| Genetic reagent (C. elegans) | eif-3.G(ju1327) II / mnC1 II; juSi366 IV; acr-2(n2420) X | This work | CZ26760 | Related to Figure 4—figure supplement 1A |
| Genetic reagent (C. elegans) | juSi364 IV; acr-2(n2420) X | This work | CZ26494 | Figure 4—figure supplement 1A |
| Genetic reagent (C. elegans) | eif-3.G(ju807)II juSi364 IV; acr-2(n2420) X | This work | CZ26243 | Related to Figure 4—figure supplement 1A |
| Genetic reagent (C. elegans) | juSi365 IV | This work | CZ26588 | Related to Figure 4—figure supplement 1A |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; juSi365 IV; acr-2(n2420) X | This work | CZ26565 | Figure 4—figure supplement 1A |
| Genetic reagent (C. elegans) | juSi365 IV; acr-2(n2420) X | This work | CZ26566 | Related to Figure 4—figure supplement 1A |
| Genetic reagent (C. elegans) | juSi368 IV | This work | CZ26656 | Related to Figure 4—figure supplement 1A |
| Genetic reagent (C. elegans) | juSi368 IV; acr-2(n2420) X | This work | CZ26623 | Figure 4—figure supplement 1A |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; juSi368 IV; acr-2(n2420) X | This work | CZ26480 | Related to Figure 4—figure supplement 1A |
| Genetic reagent (C. elegans) | wgIs506 | Sarov et al., 2006 | OP506 | Supplementary file 1 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; wgIs506 | This work | CZ27926 | Supplementary file 1 |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X; wgIs506 | This work | CZ27927 | Supplementary file 1 |
| Genetic reagent (C. elegans) | dhc-1::GFP(it45) I | Lapierre et al., 2013 | OD2955 | Supplementary file 1 |
| Genetic reagent (C. elegans) | dhc-1::GFP(it45) I; acr-2(n2420) X | This work | CZ27858 | Supplementary file 1 |
| Genetic reagent (C. elegans) | dhc-1::GFP(it45) I; eif-3.G(ju807) II; acr-2(n2420) X | This work | CZ27859 | Supplementary file 1 |
| Genetic reagent (C. elegans) | wgIs432 | Sarov et al., 2006 | OP432 | Supplementary file 1 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; wgIs432 | This work | CZ27915 | Supplementary file 1 |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X; wgIs432 | This work | CZ28021 | Supplementary file 1 |
| Genetic reagent (C. elegans) | wgIs638 | Sarov et al., 2006 | OP638 | Supplementary file 1 |
| Genetic reagent (C. elegans) | unc-119(tm4063) III;acr-2(n2420) X; wgIs638 | This work | CZ28108 | Supplementary file 1 |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X; wgIs638 | This work | CZ27916 | Supplementary file 1 |
| Genetic reagent (C. elegans) | let-607(tm1423) I; unc-119(ed3) III; vrIs121 | Sarov et al., 2006 | YL651 | Supplementary file 1 |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; let-607(tm1423) I; unc-119(ed3) III; vrIs121 | This work | CZ28143 | Supplementary file 1 |
| Genetic reagent (C. elegans) | acr-2(n2420) X; let-607(tm1423) I;unc-119(ed3) III; vrIs121 | This work | CZ28119 | Supplementary file 1 |
| Genetic reagent (C. elegans) | eif-3.G(ju807) II; acr-2(n2420) X; let-607(tm1423) I; unc-119(ed3) III; vrIs121 | This work | CZ28111 | Supplementary file 1 |
| Genetic reagent (C. elegans) | juIs172 | CGC | EE86 | |
| Genetic reagent (C. elegans) | egl-30(md186) I;dpy-20(e1282ts) IV; syIs105 | CGC | PS4263 | |
| Genetic reagent (C. elegans) | juEx7964 | McCulloch et al., 2020 | CZ27420 | |
| Genetic reagent (C. elegans) | acr-2(n2420) X; juEx7964 | McCulloch et al., 2020 | CZ27217 | |
| Genetic reagent (C. elegans) | eif-3.G(C130Y) II; acr-2(n2420) X; juEx7964 | This work | CZ28109 | Supplementary file 1 |
| Recombinant DNA reagent (plasmid) | pCZGY2729 | Andrusiak et al., 2019 | RRID:Addgene_135096 | Site-specific insertion using CRISPR/Cas9 editing of C. elegans ChrIV |
| Recombinant DNA reagent (plasmid) | pCZGY2750 | Andrusiak et al., 2019 | RRID:Addgene_135094 | Expresses Cas9 and sgRNA for editing of C. elegans ChrIV |
| Recombinant DNA reagent (plasmid) | pCZGY2727 | This work | Site-specific insertion using CRISPR/Cas9 editing of C. elegans ChrI | |
| Recombinant DNA reagent (plasmid) | pCZGY2748 | This work | Expresses Cas9 and sgRNA for editing of C. elegans ChrI |
Additional files
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Supplementary file 1
Strains used in this study.
- https://cdn.elifesciences.org/articles/68336/elife-68336-supp1-v2.docx
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Supplementary file 2
Genotyping primers used in this study.
- https://cdn.elifesciences.org/articles/68336/elife-68336-supp2-v2.docx
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Supplementary file 3
Constructs and related primers used in this study.
- https://cdn.elifesciences.org/articles/68336/elife-68336-supp3-v2.docx
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Supplementary file 4
Number of mapped reads in seCLIP replicate datasets obtained after sequencing and CLIPPER filtering.
- https://cdn.elifesciences.org/articles/68336/elife-68336-supp4-v2.docx
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Supplementary file 5
Number of read clusters detected in each dataset after subtraction of IgG control background.
- https://cdn.elifesciences.org/articles/68336/elife-68336-supp5-v2.docx
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Supplementary file 6
Number of EIF-3.G footprints detected in each dataset after subtraction of background from both IgG and ∆RRM controls.
- https://cdn.elifesciences.org/articles/68336/elife-68336-supp6-v2.docx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/68336/elife-68336-transrepform-v2.pdf
