Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Antibody | Anti-phospho-p38 (Thr180/Tyr182) (rabbit monoclonal) |
Cell Signaling Technology | Cat #4511S RRID:AB_2139682 |
WB (1:1000) |
| Antibody | Anti-p38 (rabbit polyclonal) |
Cell Signaling Technology | Cat #9212 RRID:AB_330713 |
WB (1:1000) |
| Antibody | Anti-β-actin (13E5)-HRP conjugate (rabbit monoclonal) |
Cell Signaling Technology | Cat #5125 RRID:AB_1903890 |
WB (1:1000) |
| Antibody | Anti-ASCC3 (rabbit polyclonal) |
Bethyl Laboratories | Cat #A304-014A RRID:AB_2620362 |
WB (1:1000) |
| Antibody | Anti-ZNF598 (rabbit polyclonal) |
Bethyl Laboratories | Cat #A305-108A RRID:AB_2631503 |
WB (1:2000) |
| Antibody | Anti-EDF1 (rabbit polyclonal) |
Abcam | Cat #ab174651 | WB (1:1000) |
| Antibody | Anti-RACK1 (rabbit monoclonal) |
Cell Signaling Technology | Cat #5432 RRID:AB_10705522 |
WB (1:1000) |
| Antibody | Anti-FLAG (mouse monoclonal) |
Sigma | Cat #A8592 RRID:AB_439702 |
WB (1:1000) |
| Antibody | Anti-RPL10A (rabbit polyclonal) |
Bethyl Laboratories | Cat #A305-062A RRID:AB_2631457 |
WB (1:2000) |
| Antibody | Anti-RPS10 (eS10) (rabbit polyclonal) |
LS Bio | Cat #LS-C335612-20 | WB (1:500) |
| Antibody | Anti-RPS20 (uS10) (rabbit monoclonal) |
Abcam | Cat #ab133776 RRID:AB_2714148 |
WB (1:1000) |
| Antibody | Anti-RPS3 (uS3) (rabbit polyclonal) |
Abcam | Cat #ab140688 | WB (1:2000) |
| Antibody | Anti-GIGYF2 (mouse monoclonal) |
Santa Cruz Biotechnology | Cat #Sc-393918 | WB (1:100) |
| Antibody | Anti-EIF4E2 (mouse monoclonal) |
Novus Biological | Cat #H00009470-M01 RRID:AB_1505961 |
WB (1:500) |
| Antibody | Anti-phospho-c-Jun (Ser73) (rabbit polyclonal) |
Cell Signaling | Cat #9164 RRID:AB_330892 |
WB (1:1000) |
| Antibody | Anti-c-Jun (60A8) (rabbit monoclonal) |
Cell Signaling | Cat #9165 RRID:AB_2130165 |
WB (1:1000) |
| Antibody | Anti-Strep II (rabbit polyclonal) |
Novus Biologicals | Cat #NBP2-41075 | WB (1:1000) |
| Antibody | Mouse anti-rabbit IgG-HRP (mouse monoclonal) |
Santa Cruz Biotechnology | Cat #sc-2357 RRID:AB_628497 |
WB (1:5000) |
| Antibody | Goat anti-mouse IgG2a-HRP (goat polyclonal) |
Jackson Immuno Research Laboratories Inc | Cat #115-035-2006 | WB (1:5000) |
| Antibody | anti-Diglycyl Lysine (Clone GX41) antibody (mouse monoclonal) | Millipore Sigma | Cat #MABS27 RRID:AB_10807824 |
Ubiquitin remnant immunoaffinity profiling |
| Sequence-based reagent | CRISPR: EDF1 sgRNA exon 1 | GPP, Broad Institute | EDF1 sgRNA exon 1 | 5’-GAGCGACTGGGACACGGTGA-3’ |
| Sequence-based reagent | CRISPR: EDF1 sgRNA exon 3 | GPP, Broad Institute | EDF1 sgRNA exon 3 | 5’-ACATTCTATTACCAAGAACA-3’ |
| Sequence-based reagent | siRNA: ON-TARGETplus non-targeting control pool siRNA | Horizon Discovery | Cat #D-001810-01-50 | SMARTPool |
| Sequence-based reagent | siRNA: ON-TARGETplus RACK1 siRNA | Horizon Discovery | Cat #L-006876-00-0020 | SMARTPool |
| Sequence-based reagent | siRNA: ON-TARGETplus EDF1 siRNA | Horizon Discovery | Cat #L-009697-00-0020 | SMARTPool |
| Sequence-based reagent | siRNA: ON-TARGETplus Human GIGYF2 siRNA | Horizon Discovery | Cat #L-013918-01-0020 | SMARTPool |
| Sequence-based reagent | siRNA: ON-TARGETplus Human EIF4E2 siRNA | Horizon Discovery | Cat #L-019870-01-0020 | SMARTPool |
| Recombinant DNA reagent | pCMV-GFP-2A-VHP-(KAAA)20-2A-ChFP | Juszkiewicz and Hegde, 2017 | Addgene Cat #105688 | Stalling reporter based on poly(A) sequence |
| Recombinant DNA reagent | pCMV-GFP-2A-VHP-2A-ChFP (linker control) | Juszkiewicz and Hegde, 2017 | Addgene Cat #105686 | Linker control without the internal poly(A) stalling sequence |
| Recombinant DNA reagent | psiCHECK2-Renilla-2A-3xFLAG-MsXbp1u-2A-Firefly | Han et al., 2020 | N/A | Stalling reporter based on Xbp1u peptide stalling sequence |
| Recombinant DNA reagent | psiCHECK2-Renilla-2A-3xFLAG-2A-Firefly (linker control) | This study | N/A | Linker control without the internal Xbp1u stalling sequence |
| Recombinant DNA reagent | pOG44 Flp-recombinase expression vector | Thermo Fisher | Cat #V600520 | Expression of Flp recombinase in mammalian cells when co-transfected with pcDNA5/FRT plasmid. |
| Recombinant DNA reagent | pcDNA5-FRT-tetO-FLAG-BirA*-EDF1 | This study | N/A | Human EDF1 tagged with FLAG-BirA* at the N-terminus for mammalian expression. |
| Recombinant DNA reagent | pcDNA5-FRT-tetO-EDF1-FL (full-length) Strep II | This study | N/A | Human EDF1 tagged with Strep-II at the C-terminus for mammalian expression. |
| Recombinant DNA reagent | pcDNA5-FRT-tetO-EDF1-N-term (1-74) Strep II | This study | N/A | Human EDF1 truncation (amino acids 1–74) tagged with Strep-II at the C-terminus for mammalian expression. |
| Recombinant DNA reagent | pcDNA5-FRT-tetO-EDF1-C-term (73-148) Strep II | This study | N/A | Human EDF1 truncation (amino acids 73–148) tagged with Strep-II at the C-terminus for mammalian expression. |
| Recombinant DNA reagent | pcDNA5-FRT-tetO-3xFLAG-3C-EDF1 | This study | N/A | Human EDF1 tagged with 3xFLAG-HRV-3C at the N-terminus for mammalian expression. |
| Recombinant DNA reagent | pLentiCrisprV2 | Addgene | Cat #52961 RRID:Addgene_52961 |
|
| Cell line (H. sapiens) | HEK293T WT | ATCC | CRL-3216 RRID:CVCL_0063 |
|
| Cell line (H. sapiens) | HCT116 WT | ATCC | CCL-247 RRID:CVCL_0291 |
|
| cell line (H. sapiens) | HCT116 ∆ZNF598 | Sundaramoorthy et al., 2017 | N/A | |
| cell line (H. sapiens) | HCT116 ZNF598-OE | Sundaramoorthy et al., 2017 | N/A | |
| cell line (H. sapiens) | HEK293-Flp-In T-REx-WT | Thermo Fisher |
R78007 RRID:CVCL_U427 |
|
| Cell line (H. sapiens) | HEK293-Flp-In T-REx-∆ZNF598 | Garzia et al., 2017 | N/A | |
| Cell line (H. sapiens) | HEK293-Flp-In T-REx-∆EDF1 #3–1 | This study | N/A | CRISPR/Cas9 targeting EDF1, clonal selection |
| Cell line (H. sapiens) | HEK293-Flp-In T-REx-∆EDF1∆ZNF598 #1–5 | This study | N/A | CRISPR/Cas9 targeting EDF1 and ZNF598, clonal selection |
| Cell line (H. sapiens) | HEK293-Flp-In T-REx-∆EDF1:EDF1-FL (full-length) Strep II | This study | N/A | ∆EDF1 cells co-transfected with pcDNA5-FRT-tetO-EDF1-FL (full-length) Strep II and pOG44 Flp-recombinase expression vectors, and selected with hygromycin. |
| Cell line (H. sapiens) | HEK293-Flp-In T-REx-∆EDF1:EDF1-N-term (1-74) Strep II | This study | N/A | ∆EDF1 cells co-transfected with pcDNA5-FRT-tetO-EDF1-N-term (1-74) Strep II and pOG44 Flp-recombinase expression vectors, and selected with hygromycin. |
| Cell line (H. sapiens) | HEK293-Flp-In T-REx-∆EDF1:EDF1-C-term (73-148) Strep II | This study | N/A | ∆EDF1 cells co-transfected with pcDNA5-FRT-tetO-EDF1-C-term (73-148) Strep II and pOG44 Flp-recombinase expression vectors, and selected with hygromycin. |
| Cell line (H. sapiens) | HEK293-Flp-In T-REx-3xFLAG-3C-EDF1 | This study | N/A | HEK293-Flp-In T-Rex co-transfected with pcDNA5-FRT-tetO-3xFLAG-3C-EDF1 and pOG44 Flp-recombinase expression vectors, and selected with hygromycin. |
| Chemical compound, drug | Emetine | Cayman Chemical | Cat #21048 | Used to induce ribosome collisions |
| Chemical compound, drug | Anisomycin | Sigma-Aldrich | Cat #A9789 | Used to induce ribosome collisions |
| Chemical compound, drug | Doxycycline | Sigma | D9891-10G | Used to induce gene expression in Flp-In T-Rex cell lines |
| Chemical compound, drug | Hygromycin | ThermoFisher | 10687010 | selection antibiotic |
| Chemical compound, drug | Puromycin | InvivoGen | ant-pr-1 | selection antibiotic |
| Other | Trypsin | Promega | V511C | |
| Other | Lys-C | Wako | 129–02541 | |
| Other | SUPERase•In RNase inhibitor | Ambion | AM2696 | |
| Peptide, recombinant protein | RNAse A | Ambion | AM2270 | |
| Peptide, recombinant protein | Superscript III | Invitrogen | 56575 | |
| Other | Gateway BP Clonase II Enzyme mix | ThermoFisher | 11789020 | |
| Other | Gateway LR Clonase II Enzyme Mix | ThermoFisher | 11791020 | |
| Peptide, recombinant protein | Turbo DNAse | ThermoFisher | AM2239 | |
| Other | Phosphatase inhibitor | Cell Signaling Technology | 5870S | |
| Other | cOmplete, EDTA-free Protease Inhibitor Cocktail | Roche | 5056489001 | |
| Other | Mammalian Protease Inhibitor Cocktail | Sigma | P8340-5mL | |
| Commercial assay, kit | Dual-Glo Luciferase Assay System | Promega | E2940 | |
| Commercial assay, kit | Direct-zolRNA Miniprep kit | Zymo Research | R2051 | |
| Commercial assay, kit | Zymo-Seq RiboFree Total RNA Library Kit | Zymo Research | R3000 | |
| Commercial assay, kit | Dynabeads Protein A | Thermo Fisher | 10008D | |
| Commercial assay, kit | Dynabeads Protein G | Thermo Fisher | 10009D | |
| Commercial assay, kit | ANTI-FLAG M2 Affinity Gel | Sigma-Aldrich | A2220 | |
| Commercial assay, kit | PierceStreptavidin-conjugated agarose beads | Thermo Fisher | 20353 | |
| Commercial assay, kit | TMT 6plex Label Reagent | Thermo Fisher | 90068 | |
| Commercial assay, kit | TMTpro 16plex Label Reagent | Thermo Fisher | A44520 | |
| Commercial assay, kit | 3M Empore SPE Disks C18 | Sigma | 66883 U | |
| Commercial assay, kit | Sep-Pak C18 Cartridge | Waters Corporation | WAT054960 and WAT054925 |
|
| Commercial assay, kit | High pH Reversed-Phase Peptide Fractionation Kit | Thermo Fisher | 84868 | |
| Commercial assay, kit | Pierce Quantitative Colorimetric Peptide Assay | Thermo Fisher | 23275 | |
| Software, algorithm | Maxquant | Tyanova et al., 2016a | Version 1.6.10.43 RRID:SCR_014485 |
Data analysis, mass spectrometry-based proteomics |
| Software, algorithm | Comet-based (v2018.01 rev.2) in-house software pipeline | Eng et al., 2013; Huttlin et al., 2010 | N/A | Data analysis, mass spectrometry-based proteomics |
| Software, algorithm | Perseus | Tyanova et al., 2016b | Version 1.6.10 RRID:SCR_015753 |
Statistical analysis of proteomics data |
| Software, algorithm | Differential Expression Proteomics (DEP) | Zhang et al., 2018 | N/A | Statistical analysis of proteomics data |
| Software, algorithm | InCyte software for Guava easyCyte | Millipore Sigma | 0500–4120 | Data analysis for single-cell flow-cytometry |
| Software, algorithm | STAR | Dobin et al., 2013 | STAR_2.5.3a_modified RRID:SCR_015899 |
RNA-seq aligner |
| Software, algorithm | Salmon | Patro et al., 2017 | Version 1.2.1 | Transcript quantification, RNA-seq |
| Software, algorithm | DESeq2 | Love et al., 2014 | Version 3.11 RRID:SCR_015687 |
Differential gene expression analysis, RNA-seq |
| Software, algorithm | Gencode | Frankish et al., 2019 | v33 RRID:SCR_014966 |
Genome annotation, RNA-seq |
| Software, algorithm | Custom software (Python 2.7) for RNA sequencing analysis | https://github.com/greenlabjhmi/EDF1_elife_2020 (Zinshteyn and Green, 2020; copy archived at https://github.com/elifesciences-publications/EDF1_elife_2020) | Analyses and visualization of RNA-seq data | |
| Software, algorithm | Relion | Zivanov et al., 2018 | 3.0 and 3.1 RRID:SCR_016274 |
Single particle analyses and reconstruction, cryo-EM |
| Software, algorithm | PHENIX | Adams et al., 2010 | 1.18 | Tool for automated structure refinement, cryo-EM |
| Software, algorithm | WinCOOT | Emsley et al., 2010 | 0.8.9.2 | Model building, refinement and validation, Cryo-EM |
| Software, algorithm | ChimeraX | Goddard et al., 2018 | 1.0 | Visualization of cryo-EM data |
| Software, algorithm | GraphPad Prism | GraphPad Software Inc | Version 8.4.1 | Statistical analysis, graphs |