Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Ras | BD Bioscences | Cat#610001; RRID:AB_397424 |
| Anti-NRAS | Proteintech | Cat#10724-1-AP; RRID:AB_2923963 |
| Anti-GAPDH | Cell Signaling Technology | Cat#2118; RRID:AB_561053 |
| Anti-Puromycin | Sigma | Cat#MABE343; RRID:AB_2566826 |
| Anti-p21 Waf1/Cip1 | Cell Signaling Technology | Cat#2946; RRID:AB_2260325 |
| Anti-Mouse p21 | BD Biosciences | Cat#556431; RRID:AB_396415 |
| Anti-p53 | Santa Cruz | Cat#sc-126; RRID:AB_628082 |
| Anti-p16 | Abcam | Cat#ab108349; RRID:AB_10858268 |
| Anti-gH2AX | Cell Signaling Technology | Cat#9718; RRID:AB_2118009 |
| Anti-Ubiquitin | Cell Signaling Technology | Cat#58395; RRID:AB_3075532 |
| Anti-Dyskerin | Invitrogen | Cat#PA5-28922; RRID:AB_2546398 |
| Anti-hnRNP C1/C2 | Santa Cruz | Cat#sc-32308; RRID:AB_627731 |
| Anti-RPL5 | Bethyl Laboratories | Cat#A303-933A; RRID:AB_2620282 |
| Anti-RPL11 | Proteintech | Cat#16277-1-AP; RRID:AB_2181292 |
| Anti-RPL23 | Bethyl Laboratories | Cat#A305-010A; RRID:AB_2621204 |
| Anti-α-Tubulin | Sigma | Cat#T5168; RRID:AB_477579 |
| Anti-MDM2 | Sigma | Cat#OP115; RRID:AB_564806 |
| Anti-RPL8 | Bethyl Laboratories | Cat#A305-059A; RRID:AB_2631454 |
| Anti-RPL37A | Proteintech | Cat#14660-1-AP; RRID:AB_2238668 |
| Anti-RPS5 | Bethyl Laboratories | Cat#A304-011A; RRID:AB_2620359 |
| Anti-RPS14 | Bethyl Laboratories | Cat#A304-031A; RRID:AB_2621280 |
| Anti-Nucleolin | Abcam | Cat#ab22758; RRID:AB_776878 |
| Anti-Digoxigenin | Roche | Cat#11333062910; RRID:AB_2313639 |
| Normal mouse IgG | Santa Cruz | Cat#sc-2025; RRID:AB_737182 |
| Normal rabbit IgG | Cell Signaling Technology | Cat#2729; RRID:AB_1031062 |
| Anti-Mouse secondary for Western blotting | Licor | Cat#926-68072; RRID:AB_10953628 |
| Anti-Rabbit secondary for Western blotting | Licor | Cat#926-32213; RRID:AB_621848 |
| Anti-Mouse secondary for FISH | Millipore | Cat#AP124C; RRID:AB_92459 |
| Anti-Rabbit secondary for FISH | Invitrogen | Cat#A-21206; RRID:AB_2535792 |
| Anti-Mouse secondary for Immunofluorescence | Invitrogen | Cat#A-11005; RRID:AB_2534073 |
| Bacterial and virus strains | ||
| Endura electrocompetent cells | Lucigen | Cat#60242-2 |
| E.coli Stbl3 | Invitrogen | Cat#C7373-03 |
| DH10Bac Competent Cells | Invitrogen | Cat#10361012 |
| Biological samples | ||
| Chemicals, peptides, and recombinant proteins | ||
| Dulbecco’s Modified Eagle’s Medium (DMEM) | Invitrogen | Cat#11995-073 |
| Medium 199 | Gibco | Cat#11150067 |
| Eagle’s Minimum Essential Medium (EMEM) | ATCC | Cat#30-2003 |
| Fetal Bovine Serum (FBS) | Sigma | Cat#F2442 |
| Amino acid free Dulbecco’s modified Eagle medium powder | USBiological | Cat#D9800-13 |
| Dialyzed FBS | ThermoFisher Scientific | Cat#A3382001 |
| Antibiotic-antimycotic | Gibco | Cat#15240112 |
| FuGENE HD Transfection Reagent | Promega Corporation | Cat#E2311 |
| Polybrene | Millipore | Cat#TR-1003-G |
| Puromycin | ThermoFisher Scientific | Cat#A11138-03 |
| (Z)-4-Hydroxytamoxifen | Sigma | Cat#H7904 |
| TRIzol | Invitrogen | Cat#15596026 |
| NuPAGE LDS Sample Buffer (4X) | Invitrogen | Cat#NP0007 |
| Albumin, Bovine Fraction V (BSA) | Fisher | Cat#A30075-100.0 |
| Lipofectamine 3000 Transfection Reagent | Invitrogen | Cat#L3000015 |
| Hygromycin B | Invitrogen | Cat#10687010 |
| ULTRAhyb-Oligo | Invitrogen | Cat#AM8663 |
| N-Cyclohexyl-N’-(2-morpholinoethyl)carbodiimide methyl-p-toluenesulfonate | Sigma | Cat#C106402 |
| Cycloheximide | Sigma | Cat#C1988 |
| Protease Inhibitor Cocktail Set III, EDTA-Free | Millipore | Cat#539134 |
| RNasin Ribonuclease Inhibitors | Promega | Cat#N2515 |
| SlowFade Diamond Antifade Mountant with DAPI | Invitrogen | Cat#S36964 |
| SNAP-Cell Block | New England Biolabs | Cat#S9106S |
| SNAP-Cell TMR-Star | New England Biolabs | Cat#S9105S |
| SNAP-Cell Oregon Green | New England Biolabs | Cat#S9104S |
| Poly-L-lysine | Sigma | Cat#P4832 |
| Lipofectamine RNAiMax | Invitrogen | Cat#13778150 |
| Proteinase K | New England Biolabs | Cat#P8107S |
| Cellfectin II Reagent | Gibco | Cat#10362100 |
| Sf-900 II SFM | Gibco | Cat#10902096 |
| Bio-11-UTP | Invitrogen | Cat#AM8450 |
| RNase A/T1 Mix | Thermo Scientific | Cat#EN0551 |
| IRDye 800CW Streptavidin | Licor | Cat#92632230 |
| DAPI | Invitrogen | Cat#D1306 |
| Rapamycin | Sigma | Cat#553210 |
| EDTA | Invitrogen | Cat#AM9260G |
| Etoposide | Sigma | Cat#341205 |
| Critical commercial assays | ||
| NEBuilder HiFi DNA Assembly Master Mix | New England Biolabs | Cat#E2621S |
| MasterPureTM Complete DNA Purification Kit | Lucigen | Cat#MC85200 |
| Herculase II Fusion DNA Polymerase | Agilent | Cat#600679 |
| Agencourt AMPure XP beads | Beckman Coulter Life Sciences | Cat#A63882 |
| Phusion High-Fidelity DNA Polymerase | New England Biolabs | Cat#M0530S |
| Qubit dsDNA HS Assay Kit | ThermoFisher Scientific | Cat#Q32851 |
| miRNeasy mini | QIAGEN | Cat#217004 |
| PrimeScript RT Master Mix | TaKaRa | Cat#RR036A |
| SYBR Green PCR Master Mix | Applied Biosystems | Cat#4309155 |
| Senescence β-Galactosidase Staining Kit | Cell Signaling Technology | Cat#9860 |
| Click-iT Plus EdU Cell Proliferation Kit for Imaging | Invitrogen | Cat#C10639 |
| Superscript IV Reverse Transcriptase | Invitrogen | Cat#18090010 |
| AMV Reverse Transcriptase | New England Biolabs | Cat#M0277S |
| Protein Synthesis Assay Kit | Cayman Chemical | Cat#601100 |
| TURBO DNA-free kit | Invitrogen | Cat#AM1907 |
| DIG RNA labeling mix | Roche | Cat#11277073910 |
| Click-iT Nascent RNA Capture Kit | Invitrogen | Cat#C10365 |
| Superscript VILO cDNA Synthesis Kit | Invitrogen | Cat#11754050 |
| Dual-Luciferase Reporter Assay System | Promega | Cat#E1980 |
| Dynabeads Protein G | Invitrogen | Cat#10004D |
| Dynabeads MyOne Streptavidin T1 | Invitrogen | Cat#65601 |
| Amylose Resin | New England Biolabs | Cat#E8021S |
| HiScribe T7 High Yield RNA Synthesis Kit | New England Biolabs | Cat#E2040S |
| Deposited data | ||
| CRISPRi screen | This paper | GSE232859 |
| Ribosome profiling | This paper | GSE232859 |
| RNA-sequencing | This paper | GSE232859 |
| Ribosome profiling and RNA-sequencing from p53-deficient BJ-HRASG12V cells | Loayza-Puch et al.49 | GSE45833 |
| Experimental models: Cell lines | ||
| BJ-HRASG12V | Laboratory of Reuven Agami (Voorhoeve et al.26) | N/A |
| BJ-HRASG12V-dCas9KRAB cells | This paper | N/A |
| BJ-HRASG12V SNORA13 knockout cells | This paper | N/A |
| HEK293T | ATCC | CRL-3216; RRID:CVCL_0063 |
| HEK293T-RPL28-SNAP | Laboratory of Michael Buszczak (Ni et al.50) | N/A |
| Sf9 cells | Gibco | Cat#11496015 |
| CCD-1070Sk | ATCC | CRL-2091; RRID:CVCL_2332 |
| IMR-90 | ATCC | CCL-186; RRID:CVCL_0347 |
| MEF | Laboratory of Joshua T. Mendell (Kopp et al.76) | N/A |
| Experimental models: Organisms/strains | ||
| FVB/NJ mice | The Jackson Laboratory | Cat#001800; RRID:IMSR_JAX:001800 |
| Oligonucleotides | ||
| See Table S5 | N/A | N/A |
| Recombinant DNA | ||
| pHR-SFFV-KRAB-dCas9-P2A-mCherry | Gilbert et al.77 | Addgene Plasmid #60954; RRID:Addgene_60954 |
| CRISPRi non-coding library (CRiNCL) - Common to all 7 cell lines | Liu et al.28 | Addgene Plasmid #86538; RRID:Addgene_86538 |
| CRISPRi non-coding library (CRiNCL) - iPSC & HFF | Liu et al.28 | Addgene Plasmid #86550; RRID:Addgene_86550 |
| CRISPRi non-coding library (CRiNCL) - Unique to HFF | Liu et al.28 | Addgene Plasmid #86541; RRID:Addgene_86541 |
| pCRISPRia-v2 | Horlbeck et al.79 | Addgene Plasmid #84832; RRID:Addgene_84832 |
| lentiCRISPR v2 | Sanjana et al.81 | Addgene Plasmid #52961; RRID:Addgene_52961 |
| lentiCRISPR v2-Blast | Laboratory of Mohan Babu | Addgene Plasmid #83480; RRID:Addgene_83480 |
| LcV2-Hygro | Golden et al.80 | Addgene Plasmid #91977; RRID:Addgene_91977 |
| pT/Caggs-NRASV12 | Wiesner et al.87 | Addgene Plasmid #20205; RRID:Addgene_20205 |
| pT2/shp53/GFP4 | Wiesner et al.87 | Addgene Plasmid #20208; RRID:Addgene_20208 |
| pCMV-SB100 | This paper | N/A |
| pX333 | Maddalo et al.86 | Addgene Plasmid #64073; RRID:Addgene_64073 |
| pSpCas9(BB)-2A-GFP (PX458) | Ran et al.82 | Addgene Plasmid #48138; RRID:Addgene_48138 |
| XLone-GFP | Randolph et al.83 | Addgene Plasmid #96930; RRID:Addgene_96930 |
| XLone-EPB41L4A-AS1 with SNORA13 | This paper | N/A |
| XLone-EPB41L4A-AS1 without SNORA13 | This paper | N/A |
| XLone-EPB41L4A-AS1 with SNORA13 Mut(8–12,45–49) | This paper | N/A |
| pCMV-hyPBase | Laboratory of Nancy L. Craig (Yusa et al.84) | N/A |
| PLKO.1-Scrambled | Fischer et al.85 | Addgene Plasmid #136035; RRID:Addgene_136035 |
| PLKO.1-SNORA13 WT | This paper | N/A |
| PLKO.1-SNORA13 H/ACA Mut | This paper | N/A |
| PLKO.1-SNORA13 H/ACA Del | This paper | N/A |
| MTTH-SNAP | Laboratory of Michael K. Rosen (Lin et al.95) | N/A |
| pFastBac Dual | Gibco | Cat#10712024 |
| pGL3-Renilla-Ter-Firefly | Laboratory of Joshua T. Mendell (Zhu et al.78) | N/A |
| pGL3-Renilla-noTer-Firefly | Laboratory of Joshua T. Mendell (Zhu et al.78) | N/A |
| pcDNA3 Renilla-FLAG-firefly | This paper | N/A |
| pcDNA3 Renilla-FLAG-firefly K529E | This paper | N/A |
| psPAX2 | Laboratory of Didier Trono | Addgene Plasmid #12260; RRID:Addgene_12260 |
| pMD2.G | Laboratory of Didier Trono | Addgene Plasmid #12259; RRID:Addgene_12259 |
| Software and algorithms | ||
| MAGeCK | Li et al.29 | N/A |
| STAR | Dobin et al.97 | N/A |
| RiboDiff | Zhong et al.105 | N/A |
| GraphPad Prism | GraphPad | N/A |
| FlowJo | FlowJo | N/A |
| Other | ||