KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-N6-methyladenosine | AbCam | Cat#151230; RRID:AB_2753144 |
| Mouse monoclonal anti-hsp90 | BD Biosciences | Cat#610418; RRID:AB_397798 |
| Rabbit polyclonal anti-eIF3b | Bethyl | Cat#A301-761A; RRID:AB_1210995 |
| Mouse monoclonal anti-ATF4 | Cell Signaling Technology | Cat#11815; RRID:AB_2616025 |
| Rabbit monoclonal anti-phospho-GCN2 | Cell Signaling Technology | Cat#94668; RRID:n/a |
| Rabbit polyclonal anti-GCN2 | Invitrogen | Cat#PA5-17523; RRID:AB_10983800 |
| Rabbit monoclonal anti-PERK | Cell Signaling Technology | Cat#C33E10; RRID:n/a |
| Rabbit polyclonal anti-rpS19 | Proteintech | Cat#15085-1-AP; RRID:AB_2180202 |
| Rabbit polyclonal anti-eIF2α | Proteintech | Cat#11170-1-AP; RRID:AB_2096489 |
| Rabbit monoclonal anti-ALKBH5 | Invitrogen | Cat#10H24L9; RRID:n/a |
| Goat anti-Rabbit HRP | Invitrogen | Cat#31462; RRID:AB_228338 |
| Goat anti-Mouse HRP | Invitrogen | Cat#31432; RRID:AB_228302 |
| Chemicals, peptides, and recombinant proteins | ||
| Fetal Bovine Serum | Biowest | Cat#S1620 |
| Thapsigargin | Cayman Chemical | Cat#10522 |
| Tunicamycin | Cayman Chemical | Cat#11445 |
| PERKi (GSK2656157) | MedChemExpress | Cat#HY-13820 |
| GCN2iB | MedChemExpress | Cat#HY-112654 |
| Cap-Clip Acid Pyrophosphatase | Cellscript | Cat#C-CC15011H |
| Bovine-Serum Albumin | Chemimpex | Cat#00577 |
| DTT | Chemimpex | Cat#00127 |
| Hybond-N+ membrane | Cytiva | Cat#RPN303B |
| Trypsin | Genesee | Cat#25-510 |
| Penicillin-streptomycin | Genesee | Cat#25-512 |
| Random Hexamer | Integrated DNA Technologies | Cat#51-01-18-01 |
| Murine RNase inhibitor | New England Biolabs | Cat#M0314L |
| Luna Universal qPCR master mix | New England Biolabs | Cat#M3003E |
| m7GpppG | New England Biolabs | Cat#S1411L |
| GpppG | New England Biolabs | Cat#S1407L |
| Q5 polymerase | New England Biolabs | Cat#M0491L |
| Vaccinia capping enzyme | New England Biolabs | Cat#M2080S |
| 2′ O-Methyltransferase enzyme | New England Biolabs | Cat#M0366S |
| Antarctic phosphatase | New England Biolabs | Cat#MO289L |
| T4 PNK | New England Biolabs | Cat#M0201L |
| XRN-1 | New England Biolabs | Cat#M0338L |
| 32P Radionuclide | Perkin-Elmer | Cat#NEX053H001MC |
| [ɑ-32P]-GTP | Perkin-Elmer | Cat#BLU006H250UC |
| Polyethylenimine, Linear, MW 25,000 | Polysciences, Inc | Cat#23966-1 |
| PhosSTOP | Sigma Aldrich | Cat#4906837001 |
| DMEM | Gibco | Cat#11995073 |
| OptiMEM | Gibco | Cat#11058021 |
| DMSO | ThermoFisher Scientific | Cat#BP231100 |
| Puromycin Dihydrochloride | ThermoFisher Scientific | Cat#AAJ61278MC |
| Sera-Mag Protein A/G beads | Cytiva | Cat#09-981-921 |
| Anti-HA magnetic beads | ThermoFisher Scientific, Pierce | Cat#PI88837 |
| SeraMag Oligo dT magnetic beads | Cytiva | Cat#09-981-145 |
| G-25 column | Cytiva | Cat#45 001 397 |
| Heparin | ThermoFisher Scientific | Cat#BP2425 |
| Cycloheximide | MP Biomedicals, Inc. | Cat#ICN10018301 |
| Phos-Tag acrylamide | Apexbio Technology | Cat#NC1646902 |
| SUPERase-In RNase Inhibitor | Invitrogen | Cat#AM2696 |
| Proteinase K | ThermoFisher Scientific | Cat#BP1700-100 |
| Phenol Chloroform | VWR | Cat#97064-712 |
| Glycogen | VWR | Cat#97063-256 |
| HIV-1 Protease | C. Schiffer, University of Massachusetts Medical School | |
| NEBuilder HiFi DNA Assembly | NEB | Cat#E2621L |
| EXPRE35S35S Protein Labeling Mix | Perkin Elmer | Cat#NEG072002MC |
| Critical commercial assays | ||
| NEBNext Ultra II Directional RNA Library Prep Kit for Illumina | New England Biolabs | Cat#E7760L |
| m6A eCLIP Kit | Eclipse Bioinnovations | Cat#143651 |
| Deposited data | ||
| RNA-Seq (WT versus phosphomimetic eIF3d HEK293T, veh. versus 16 h Tg) | This paper | GSE236188 |
| eIF3dTEV Subunit-Seq (HEK293T 16h Tg) | This paper | GSE236188 |
| m6A eCLIP (WT versus phosphomimetic eIF3d HEK293T, veh. versus 16 h Tg) | This paper | GSE236188 |
| Experimental models: Cell lines | ||
| Human: HEK293T | ATCC | CRL-11268 |
| Human: HEK293T eIF3dTEV | Lamper et al23 | |
| Human: HEK293T eIF3d S528D/S529D | This paper | |
| Human: HEK293T ALKBH5-ΔSL3 | This paper | |
| Oligonucleotides | ||
| DNA primers for RT-qPCR, see Table S4 | This paper | Table S4 |
| DNA primers for ALKBH5 cloning, see Table S4 | This paper | Table S4 |
| DNA primers for ATF4 cloning, see Table S4 | This paper | Table S4 |
| DNA primers for GCN2 cloning, see Table S4 | This paper | Table S4 |
| sgRNA sequences (eIF3d and ALKBH5), see Table S4 | This paper | Table S4 |
| Donor oligos (eIF3d and ALKBH5), see Table S4 | This paper | Table S4 |
| Recombinant DNA | ||
| Plasmid: pLBH269 SpCas9 sgRNA | L. Harrington and J. Doudna (UC Berkeley) | |
| Plasmid: pcDNA4-ALKBH5 5′ UTR-RLuc | This paper | |
| Plasmid: pcDNA4-ALKBH5 5′ UTR-RLuc – stem | This paper | |
| Plasmid: pcDNA4-ALKBH5 5′ UTR-RLuc – comp | This paper | |
| Plasmid: pcDNA4-ALKBH5 5′ UTR-RLuc – loop | This paper | |
| Plasmid: pcDNA4-GCN2 5′ UTR-RLuc | This paper | |
| Plasmid: pcDNA4-ATF4 5′ UTR-RLuc | This paper | |
| Plasmid: pGEX-4T1-PCIF1 | Boulias et al.48 | E. Greer, Washington University, St. Louis |
| Software and algorithms | ||
| CFX Maestro | Biorad | |
| Windaq | DataQ instruments | |
| RNAStructure | Reuter et al.75 | https://rna.urmc.rochester.edu/RNAstructure.html |
| VARNA | Darty et al.74 | https://varna.lri.fr |
| DAVID | Dennis et al.90 | https://david.ncifcrf.gov |
| ShinyGO | Ge et al.89 | http://bioinformatics.sdstate.edu/go/ |
| DESeq2 | Love et al.82 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Bowtie2 | Langmead et al.78 | https://bowtie-bio.sourceforge.net/bowtie2 |
| bwa | Li et al.86 | https://bio-bwa.sourceforge.net |
| Cutadapt | Martin77 | https://pypi.org/project/cutadapt/ |
| SAMtools | Li et al.80 | http://www.htslib.org |
| STAR | Dobin et al.79 | https://github.com/alexdobin/STAR |
| UMItools | Smith et al.84 | https://github.com/CGATOxford/UMI-tools |
| pyCRAC | Webb et al.85 | https://sandergranneman.bio.ed.ac.uk/pycrac-software |
| CTK | Shah et al.87 | https://zhanglab.c2b2.columbia.edu/index.php/CTK_Documentation |