KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-6xHis-tag | Abcam | ab18184; RRID:AB_444306 |
| Anti-FLAG | Sigma-Aldrich | F7425; RRID:AB_439687 |
| Anti-RRP4 (EXOSC2) | Abcam | ab111810; RRID:AB_10862519 |
| Anti-EXOSC3 | Abcam | ab156683; RRID:AB_2619635 |
| Anti-RRP41 (EXOSC4) | Abcam | ab137250 |
| Anti-EXOSC5 | Abcam | ab69699; RRID:AB_1268842 |
| Anti-EXOSC9 | Abcam | ab176802 |
| Anti-Dis3L1 | Abcam | ab89042; RRID:AB_2040576 |
| Anti-WDR61 antibody | Abcam | ab57840; RRID:AB_946149 |
| Anti-SKI2W antibody | MilliporeSigma | MABE1048 |
| Anti-SKI3 antibody | ThermoFisher Scientific | PA5-40078 RRID:AB_2607233 |
| ECL anti-Rabbit IgG HRP-linked whole Ab | GE Healthcare | NA934; RRID:AB_772206 |
| Anti-Mouse IgG-Peroxidase Ab | Sigma-Aldrich | A9044; RRID:AB_258431 |
| Bacterial and Virus Strains | ||
| E.coli DH5α | Invitrogen | 18265017 |
| E.coli BL21 Star (DE3) | Invitrogen | C601003 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Rabbit reticulocyte lysate | Green Hectares | n/a |
| Flexi Rabbit Reticulocyte Lysate System | Promega | L4540 |
| tRNA calf liver | Promega | Y209X |
| Gibco-Penicillin-Streptomycin | Fisher Scientific/Life Technologies | 15-140-163 |
| Gibco-GlutaMAX-Supplement | Fisher Scientific/Life Technologies | 35 050 079 |
| Gibco-Dulbecco’s Modified Eagle Medium | Fisher Scientific/Life Technologies | 11 960 069 |
| Gibco-Fetal Bovine Serum | Fisher Scientific/Life Technologies | 26-140-079 |
| Lipofectamine 3000 | Fisher Scientific/Life Technologies | L3000075 |
| Spermidine Trihydrochloride | Fisher Scientific | AC21510-0050 |
| Isopropyl-beta-D-thiogalactoside | Gold Biotechnology | I2481C100 |
| Anti-FLAG M2 Affinity Gel | Sigma-Aldrich | A2220 |
| 3x Flag peptide | Sigma-Aldrich | F4799 |
| BM Chemiluminescence Blotting Substrate | Roche | 11500694001 |
| Ni-NTA Agarose | QIAGEN | 30230 |
| MonoS 5/50 GL column | GE Healthcare Life Sciences | 17516801 |
| MonoQ 5/50 GL column | GE Healthcare Life Sciences | 17516601 |
| Superdex 200 Increase 5/150 GL | GE Healthcare Life Sciences | 28990945 |
| RiboLock RNase inhibitor | Thermo Scientific | EO0381 |
| T7 RNA polymerase | Thermo Scientific | EP0111 |
| Avian Myeloblastosis Virus Reverse Transcriptase | Promega | M5108 |
| T7 mScript-Standard mRNA Production System | Cellscript | C-MSC100625 |
| BspQI | New England Biolabs | R0712S |
| BstNI | New England Biolabs | R0607S |
| EcoRI | New England Biolabs | R0101S |
| HindIII | New England Biolabs | R0104S |
| T4 Polynucleotide Kinase | New England Biolabs | M0201S |
| Casein Kinase II | New England Biolabs | P6010S |
| [γ32P]ATP | Perkin Elmer | BLU002Z |
| [α32P]GTP | Perkin Elmer | BLU006H500UC |
| [35S]-methionine | Perkin Elmer | NEG009T |
| Deposited Data | ||
| Raw data | Mendeley data | https://data.mendeley.com/datasets/k5s73hjmkj/draft?a=188bd905-9c0c-424c-9856-e9f4563bffa2 |
| Experimental Models: Cell Lines | ||
| HEK293T cells | ATCC | CRL-3216; RRID:CVCL_0063 |
| Oligonucleotides | ||
| ssRNA (CUGAGGACUU) | Dharmacon | n/a |
| ssRNA (CCGCAGCCC) | Dharmacon | n/a |
| ssRNA (GCAGCCC) | Dharmacon | n/a |
| Recombinant DNA | ||
| pET28a-His6-EXOSC1 | This study | |
| pET3a-EXOSC2-His6 | This study | |
| pET28a-His6-EXOSC3 | This study | |
| pET28a-His6-EXOSC5 | This study | |
| pET28a-EXOSC8-His6 | This study | |
| pETDuet-ExoSc9-Flag-EXOSC4-His6 | This study | |
| pETDuet-ExoSc6-Flag-EXOSC7 | This study | |
| pcDNA3.1-Dis3L1-FLAG | This study | |
| pcDNA3.1-FLAG-WDR61 | This study | |
| pET28a-His6-WDR61-FLAG-His6 | This study | |
| pET14b-His6-eIF6 | This study | |
| pQE31-His6-eIF1 | Pisarev et al., 2007a | |
| pET28-His6-eIF1A | Pisarev et al., 2007a | |
| pET15b-His6-eIF4A | Pisarev et al., 2007a | |
| pET15b-His6-eIF4B | Pisarev et al., 2007a | |
| pET28-His6-eIF4G736-1115 | Pisarev et al., 2007a | |
| pET19b-His6-eIF5 | Pisarev et al., 2007a | |
| pET23b-eRF1-His6 | Alkalaeva et al., 2006 | |
| pQE-30-His6-eRF1(AGQ) | Alkalaeva et al., 2006 | |
| pET23b-eRF3Cp-His6 | Alkalaeva et al., 2006 | |
| pFL-B31cl-Pelota-His6 | Pisareva et al., 2011 | |
| pFL-B31cl-Hbs1-His6 | Pisareva et al., 2011 | |
| pcDNA-3xFLAG-ABCE1 | Shao and Hegde, 2014 | |
| pUC57-β-globin-30 bases | This study | |
| pUC57-β-globin-30-(A)50 bases | This study | |
| pUC57-β-globin-10 bases | This study | |
| pUC57-β-globin-50 bases | This study | |
| pUC57-MF-Stop | Zinoviev et al., 2018 | |
| pUC57-MLLSSF-Stop | Zinoviev et al., 2018 | |
| pUC57-MVLL-Stop | This study | |
| pUC57-MLLFF-Stop-(A50) | This study | |
| pUC57-[7nt-3’UTR MLLFF-Stop] | This study | |
| pUC57-[27nt-3’UTR MLLFF-Stop] | This study | |
| pUC57-[47nt-3’UTR MLLFF-Stop] | This study | |
| pUC57-β-VHP(75aa) | Kuroha et al., 2018 | |
| pUC57-β-VHP(25aa) | This study | |
| pTRM1(pBR322-tRNAiMet) | Pestova and Hellen, 2001 | |
| pUC57-[tRNASer-AGA] | Zinoviev et al., 2015 | |
| pUC57-[tRNALeu-AAG] | Pisarev et al., 2010 | |
| pUC57-[tRNAPhe-GAA] | Zinoviev et al., 2018 | |
| Software and Algorithms | ||
| ImageQuant TL version 8.1 | GE Healthcare | RRID:SCR_014246 |
| Mfold | http://unafold.rna.albany.edu/?q=mfold/download-mfold | RRID:SCR_008543 |