Eukaryotic initiation factor EIF-3.G augments mRNA translation efficiency to regulate neuronal activity

  1. Stephen M Blazie
  2. Seika Takayanagi-Kiya
  3. Katherine A McCulloch
  4. Yishi Jin  Is a corresponding author
  1. Section of Neurobiology, Division of Biological Sciences, University of California San Diego, United States
7 figures, 4 videos, 1 table and 7 additional files

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;

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
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
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 …

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
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 …

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
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
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: …

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
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
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
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 …

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 …

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
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
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
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
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 …

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
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)…

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
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
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
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
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
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 …

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 …

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 …

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.

https://cdn.elifesciences.org/articles/68336/elife-68336-fig6-figsupp1-data1-v2.xlsx
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 …

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
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 …

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
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
DesignationSource or referenceIdentifiersAdditional information
Antibodyanti-FLAG (Rabbit)Sigma-AldrichCat# F7425, RRID:AB_439687WB (1:2000)
Antibodyanti-Actin clone C4 (Mouse monoclonal)MP BiomedicalsCat# 08691002, RRID:AB_2335304WB (1:2000)
AntibodyAnti-FLAG M2 Magnetic BeadsSigma-AldrichCat# M8823, RRID:AB_2637089IP
Recombinant protein reagentCas9-NLS (purified protein)UC Berkely QB3
Genetic reagent
(C. elegans)
+CGCRRID:CGC_N2
Genetic reagent
(C. elegans)
acr-2(n2420) XJospin et al., 2009MT6241
Genetic reagent
(C. elegans)
eif-3.G(ju807) IIThis workCZ22197Figure 1F
Genetic reagent
(C. elegans)
eif-3.G(ju1840) IIThis workCZ28494Figure 1C
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) XThis workCZ21759Figure 1C
Genetic reagent
(C. elegans)
eif-3.G(ju1840) II; acr-2(n2420) XThis workCZ28495Figure 1C
Genetic reagent
(C. elegans)
eif-3.G(ju1327) / mnC1 IIThis workCZ22974Figure 1F
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx7015This workCZ22976Figure 1C
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx7016This workCZ22977Figure 1C
Genetic reagent
(C. elegans)
eif-3.G(ju807) I;acr-2(n2420) X; juEx7045This workCZ23125Figure 1E
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) X; juEx7046This workCZ23126Figure 1E
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) X; juEx7019This workCZ22980Figure 1E
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) X; juEx7020This workCZ22981Figure 1E
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) X; juEx7439This workCZ23791Figure 1E
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) X; juEx7440This workCZ23880Figure 1E
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) X; juEx7021This workCZ22982Figure 1E
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) X; juEx7022This workCZ22983Figure 1E
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) X; juEx8062This workCZ27881Figure 1E
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) X; juEx8063This workCZ27882Figure 1E
Genetic reagent
(C. elegans)
eif-3.G(ju1327) /mnC1 II; acr-2(n2420) XThis workCZ23310Figure 1F
Genetic reagent
(C. elegans)
eif-3.G(ju807) / eif-3.G(ju1327) IIThis workCZ25714Figure 1F
Genetic reagent
(C. elegans)
eif-3.G(ju807) / eif-3.G(ju1327) II; acr-2(n2420) XThis workCZ26828Figure 1F
Genetic reagent
(C. elegans)
juSi320 IVThis workCZ24063Figure 2B; Figure 1—figure supplement 1B
Genetic reagent
(C. elegans)
eif-3.G(ju1327) /mnC1 II; juSi320 IVThis workCZ24079Figure 2A
Genetic reagent
(C. elegans)
juSi320 IV; acr-2(n2420) XThis workCZ24729Figure 2A
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; juSi320 IV; acr-2(n2420) XThis workCZ28107Figure 2A
Genetic reagent
(C. elegans)
juSi331 IVThis workCZ24651Figure 2B; Figure 1—figure supplement 1B
Genetic reagent
(C. elegans)
juSi331 IV; acr-2(n2420) XThis workCZ24652Figure 2A
Genetic reagent
(C. elegans)
eif-3.G(ju1327) / mnC1 II; juSi331 IV; acr-2(n2420) XThis workCZ28497Figure 2A
Genetic reagent
(C. elegans)
juIs14 IVWang et al., 2017CZ631
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; juIs14 IVThis workCZ24161Figure 1—figure supplement 2
Genetic reagent
(C. elegans)
juIs14 IV; acr-2(n2420) XMcCulloch et al., 2020CZ5808
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; juIs14 IV; acr-2(n2420) XThis workCZ8905Figure 1—figure supplement 2A
Genetic reagent
(C. elegans)
nuIs94Hallam et al., 2000KP2229
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; nuIs94This workCZ24021Figure 1—figure supplement 2B
Genetic reagent
(C. elegans)
acr-2(n2420) X; nuIs94This workCZ5815Figure 1—figure supplement 2B
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420)X; nuIs94This workCZ24021Figure 1—figure supplement 2B
Genetic reagent
(C. elegans)
eif-3.E(ok2607) I / hT2 I,III; acr-2(n2420) XThis workCZ27434Figure 1—figure supplement 3A
Genetic reagent
(C. elegans)
eif-3.E(ok2607) I / hT2 I, III; eif-3.G(ju807) II; acr-2(n2420) XThis workCZ27433Figure 1—figure supplement 3A
Genetic reagent
(C. elegans)
eif-3.H(ok1353) I / hT2 I, III; acr-2(n2420) XThis workCZ27435Figure 1—figure supplement 3A
Genetic reagent
(C. elegans)
eif-3.H(ok1353) I / hT2 I, III; eif-3.G(ju807) II; acr-2(n2420) XThis workCZ27436Figure 1—figure supplement 3A
Genetic reagent
(C. elegans)
oxSi39 IVQi et al., 2013CZ12338
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; oxSi39 IVThis workCZ23854Figure 1—figure supplement 3B
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx7056This workCZ23203Figure 3
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx7057This workCZ23204Figure 3
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx8100This workCZ28152Figure 3
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx8101This workCZ28153Figure 3
Genetic reagent
(C. elegans)
juEx7113This workCZ26777Figure 3
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx7114This workCZ23304Figure 3
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx7115This workCZ23305Figure 3
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx8095This workCZ28066Figure 3
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx8096This workCZ28067Figure 3
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx8087This workCZ28057Figure 3
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx8088This workCZ28058Figure 3
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx8089This workCZ28064Figure 3
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx8090This workCZ28065Figure 3
Genetic reagent
(C. elegans)
unc-119(tm4063) III; wgIs433Sarov et al., 2006OP433
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; unc-119(tm4063)III; wgIs433This workCZ28145Figure 6C
Genetic reagent
(C. elegans)
acr-2(n2420) X; unc-119(tm4063) III; wgIs433This workCZ27913Figure 6C
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; unc-119(tm4063) III; acr-2(n2420) X; wgIs433This workCZ27914Figure 6C
Genetic reagent
(C. elegans)
sqIs17Dittman and Kaplan, 2006MAH240
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; sqIs17This workCZ28334Figure 6—figure supplement 1
Genetic reagent
(C. elegans)
acr-2(n2420) X; sqIs17This workCZ28212Figure 6—figure supplement 1
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) X; sqIs17This workCZ28218Figure 6—figure supplement 1
Genetic reagent
(C. elegans)
unc-13(s69) I; wgIs433This workCZ28491Figure 6C
Genetic reagent
(C. elegans)
unc-13(s69) I; acr-2(n2420) X; wgIs433This workCZ28492Figure 6C
Genetic reagent
(C. elegans)
unc-13(s69) I; eif-3.G(ju807); acr-2(n2420) X; wgIs433This workCZ28493Figure 6C
Genetic reagent
(C. elegans)
juSi260 ncs-2(tm1943) IZhou et al., 2017CZ22459
Genetic reagent
(C. elegans)
juSi260 ncs-2(tm1943) I; eif-3.G(ju807) IIThis workCZ23225Figure 7B
Genetic reagent
(C. elegans)
juSi260 ncs-2(tm1943) I; acr-2(n2420) XThis workCZ22345Figure 7B
Genetic reagent
(C. elegans)
juSi260 ncs-2(tm1943) I; eif-3.G(ju807) II; acr-2(n2420) XThis workCZ28110Figure 7B
Genetic reagent
(C. elegans)
juSi391 ncs-2(tm1943) IThis workCZ28213Figure 7C
Genetic reagent
(C. elegans)
juSi391 ncs-2(tm1943) I; eif-3.G(ju807) IIThis workCZ28340Figure 7C
Genetic reagent
(C. elegans)
juSi391 ncs-2(tm1943) I;acr-2(n2420) XThis workCZ28252Figure 7C
Genetic reagent
(C. elegans)
juSi391 ncs-2(tm1943) I;eif-3.G(ju807) II; acr-2(n2420) XThis workCZ28253Figure 7C
Genetic reagent
(C. elegans)
juSi392 ncs-2(tm1943) IThis workCZ28277Figure 7—figure supplement 1B
Genetic reagent
(C. elegans)
juSi392 ncs-2(tm1943) I;eif-3.G(ju807) IIThis workCZ28312Figure 7—figure supplement 1B
Genetic reagent
(C. elegans)
juSi392 ncs-2(tm1943) I; acr-2(n2420) XThis workCZ28291Figure 7—figure supplement 1B
Genetic reagent
(C. elegans)
juSi392 ncs-2(tm1943) I; eif-3.G(ju807) II; acr-2(n2420) XThis workCZ28292Figure 7—figure supplement 1B
Genetic reagent
(C. elegans)
juSi393 ncs-2(tm1943) IThis workCZ28278Figure 7—figure supplement 1C
Genetic reagent
(C. elegans)
juSi393 ncs-2(tm1943) I; eif-3.G(ju807) IIThis workCZ28311Figure 7—figure supplement 1C
Genetic reagent
(C. elegans)
juSi393 ncs-2(tm1943) I; acr-2(n2420) XThis workCZ28293Figure 7—figure supplement 1C
Genetic reagent
(C. elegans)
juSi393 ncs-2(tm1943) I; eif-3.G(ju807) II; acr-2(n2420) XThis workCZ28294Figure 7—figure supplement 1C
Genetic reagent
(C. elegans)
juEx2045---CZ9635
Genetic reagent
(C. elegans)
hlh-30(tm1978) IVCGCCZ23321
Genetic reagent
(C. elegans)
hlh-30(tm1978) IV; acr-2(n2420) XThis workCZ28174Related to Figure 6C
Genetic reagent (C. elegans)eif-3.G(ju807) II; hlh-30(tm1978) IV; acr-2(n2420) XThis workCZ28175Related to Figure 6C
Genetic reagent
(C. elegans)
eif-3.G(ju1327) II /mnC1; juSi363 IV; acr-2(n2420) XThis workCZ26759Related to Figure 4—figure supplement 1A
Genetic reagent
(C. elegans)
eif-3.G(ju1327) II / mnC1 II; juSi366 IV; acr-2(n2420) XThis workCZ26760Related to Figure 4—figure supplement 1A
Genetic reagent
(C. elegans)
juSi364 IV; acr-2(n2420) XThis workCZ26494Figure 4—figure supplement 1A
Genetic reagent (C. elegans)eif-3.G(ju807)II juSi364 IV; acr-2(n2420) XThis workCZ26243Related to Figure 4—figure supplement 1A
Genetic reagent
(C. elegans)
juSi365 IVThis workCZ26588Related to Figure 4—figure supplement 1A
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; juSi365 IV; acr-2(n2420) XThis workCZ26565Figure 4—figure supplement 1A
Genetic reagent
(C. elegans)
juSi365 IV; acr-2(n2420) XThis workCZ26566Related to Figure 4—figure supplement 1A
Genetic reagent
(C. elegans)
juSi368 IVThis workCZ26656Related to Figure 4—figure supplement 1A
Genetic reagent
(C. elegans)
juSi368 IV; acr-2(n2420) XThis workCZ26623Figure 4—figure supplement 1A
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; juSi368 IV; acr-2(n2420) XThis workCZ26480Related to Figure 4—figure supplement 1A
Genetic reagent
(C. elegans)
wgIs506Sarov et al., 2006OP506Supplementary file 1
Genetic reagent (C. elegans)acr-2(n2420) X; wgIs506This workCZ27926Supplementary file 1
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) X; wgIs506This workCZ27927Supplementary file 1
Genetic reagent
(C. elegans)
dhc-1::GFP(it45) ILapierre et al., 2013OD2955Supplementary file 1
Genetic reagent
(C. elegans)
dhc-1::GFP(it45) I; acr-2(n2420) XThis workCZ27858Supplementary file 1
Genetic reagent (C. elegans)dhc-1::GFP(it45) I; eif-3.G(ju807) II; acr-2(n2420) XThis workCZ27859Supplementary file 1
Genetic reagent
(C. elegans)
wgIs432Sarov et al., 2006OP432Supplementary file 1
Genetic reagent
(C. elegans)
acr-2(n2420) X; wgIs432This workCZ27915Supplementary file 1
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) X; wgIs432This workCZ28021Supplementary file 1
Genetic reagent
(C. elegans)
wgIs638Sarov et al., 2006OP638Supplementary file 1
Genetic reagent
(C. elegans)
unc-119(tm4063) III;acr-2(n2420) X; wgIs638This workCZ28108Supplementary file 1
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) X; wgIs638This workCZ27916Supplementary file 1
Genetic reagent
(C. elegans)
let-607(tm1423) I; unc-119(ed3) III; vrIs121Sarov et al., 2006YL651Supplementary file 1
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; let-607(tm1423) I; unc-119(ed3) III; vrIs121This workCZ28143Supplementary file 1
Genetic reagent
(C. elegans)
acr-2(n2420) X; let-607(tm1423) I;unc-119(ed3) III; vrIs121This workCZ28119Supplementary file 1
Genetic reagent
(C. elegans)
eif-3.G(ju807) II; acr-2(n2420) X; let-607(tm1423) I; unc-119(ed3) III; vrIs121This workCZ28111Supplementary file 1
Genetic reagent
(C. elegans)
juIs172CGCEE86
Genetic reagent
(C. elegans)
egl-30(md186) I;dpy-20(e1282ts) IV; syIs105CGCPS4263
Genetic reagent
(C. elegans)
juEx7964McCulloch et al., 2020CZ27420
Genetic reagent
(C. elegans)
acr-2(n2420) X; juEx7964McCulloch et al., 2020CZ27217
Genetic reagent
(C. elegans)
eif-3.G(C130Y) II; acr-2(n2420) X; juEx7964This workCZ28109Supplementary file 1
Recombinant DNA reagent (plasmid)pCZGY2729Andrusiak et al., 2019RRID:Addgene_135096Site-specific insertion using CRISPR/Cas9 editing of C. elegans ChrIV
Recombinant DNA reagent (plasmid)pCZGY2750Andrusiak et al., 2019RRID:Addgene_135094Expresses Cas9 and sgRNA for editing of C. elegans ChrIV
Recombinant DNA reagent (plasmid)pCZGY2727This workSite-specific insertion using CRISPR/Cas9 editing of C. elegans ChrI
Recombinant DNA reagent (plasmid)pCZGY2748This workExpresses Cas9 and sgRNA for editing of C. elegans ChrI

Additional files

Supplementary file 1

Strains used in this study.

https://cdn.elifesciences.org/articles/68336/elife-68336-supp1-v2.docx
Supplementary file 2

Genotyping primers used in this study.

https://cdn.elifesciences.org/articles/68336/elife-68336-supp2-v2.docx
Supplementary file 3

Constructs and related primers used in this study.

https://cdn.elifesciences.org/articles/68336/elife-68336-supp3-v2.docx
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
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
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
Transparent reporting form
https://cdn.elifesciences.org/articles/68336/elife-68336-transrepform-v2.pdf

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