KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| p53 antibody (CM5) | Leica (Novocastra) | NCL-L-p53-CM5p; RRID: AB_563933 |
| p53 antibody (1C12) | Cell Signaling Technology | 2524; RRID: AB_331743 |
| METTL3 polyclonal antibody | Abclonal | A8370; RRID: AB_2770344 |
| METTL3 monoclonal antibody | Abcam | ab195352; RRID: AB_2721254 |
| HA antibody | Thermo Fisher Scientific | 71–5500; RRID: AB_2533988 |
| FLAG antibody | Sigma-Aldrich | F1804; RRID: AB_262044 |
| MDM2 antibody (2A10) | Abcam | ab16895; RRID: AB_2143534 |
| GAPDH antibody | Fitzgerald | 10R-G109A; RRID: AB_1285808 |
| N6-Methyladenosine (m6A) (D9D9W) antibody | Cell Signaling Technology | 56593; RRID: AB_2799515 |
| Goat anti-rabbit HRP antibody | Jackson ImmunoResearch | 111-035-144; RRID: AB_2307391 |
| Goat anti-mouse HRP antibody | Jackson ImmunoResearch | 115-035-003; RRID: AB_10015289 |
| Peroxidase AffiniPure Goat Anti-Mouse IgG, light chain specific | Jackson ImmunoResearch | 115-035-174; RRID: AB_2338512 |
| Peroxidase IgG Fraction Monoclonal Mouse Anti-Rabbit IgG, light chain specific | Jackson ImmunoResearch | 211-032-171; RRID: AB_2339149 |
| Bacterial and virus strains | ||
| Ad-Cre or Ad5CMVCre | University of Iowa | VVC-U of Iowa-5 |
| Lenti-U6-sgMettl3/Cre | This paper | N/A |
| Lenti-U6-sgNeoR1/Cre | Laboratory of Dr. Monte Winslow | N/A |
| E.coli BL21 expressing GST-0 | Laboratory of Dr. Hua Lu and Shelya Zeng | N/A |
| E.coli BL21 expressing GST-p53 | Laboratory of Dr. Hua Lu and Shelya Zeng | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Lipofectamine 2000 | Thermo Fisher Scientific | 11668019 |
| Doxorubicin hydrochloride | Sigma-Aldrich | D1515 |
| Puromycin dihydrochloride | Sigma-Aldrich | P7255 |
| Cycloheximide | Sigma-Aldrich | C7698 |
| Glutathione Sepharose 4B | Cytiva | 17-0756-01 |
| GST-0 | This paper | N/A |
| GST-p53 | This paper | N/A |
| 6X-His-HDM2 | Laboratory of Dr. Hua Lu and Shelya Zeng | N/A |
| Critical commercial assays | ||
| Clarity Western ECL Substrate | Bio-Rad | 1705060 |
| ECL Prime Western Blotting System | Millipore-Sigma | GERPN2232 |
| Pierce BCA Protein Assay Kit | Thermo Fisher Scientific | 23227 |
| TRIzol reagent | Thermo Fisher | 15596026 |
| PowerUP SYBR green master mix | Thermo Fisher | 4367660 |
| M-MLV Reverse Transcriptase | Thermo Fisher | 28025013 |
| iScript Supermix cDNA synthesis kit | Bio-Rad | 1708841 |
| Gateway BP Clonase II Enzyme Mix | Thermo Fisher | 11789-020 |
| Gateway LR Clonase II Enzyme Mix | Thermo Fisher | 11791-020 |
| Q5 Site-directed mutagenesis kit | NEB | E0554S |
| TNT SP6 High-Yield Wheat Germ Protein Expression System | Promega | L3260 |
| Deposited data | ||
| M6A-eCLIP-seq and RNA-seq | This paper | GEO:GSE169343 |
| shLuc and shMettl3 MEF RNA-seq | This paper | GEO:GSE193341 |
| Mendeley Data | This paper | Mendeley Data: https://dx.doi.org/10.17632/gdpmnddt7v.1 |
| Mouse p53 ChIP-seq | Kenzelmann-Broz et al. (2013) | GEO:GSE46240 |
| E1A;HRasG12V p53WT and p53 null MEF RNA-seq | Valente et al. (2020) | GEO:GSE136355 |
| Achilles DepMap (CCLE_Depmap_21Q4 release) | Meyers et al. (2017) | DepMap: http://depmap.org |
| Scripts used in the study | This paper | GitHub: https://github.com/CancerCompBioLab/Mettl3_paper |
| Experimental models: Cell lines | ||
| Mouse: E1A;HRasG12V p53WT MEFs | Laboratory of Dr. Laura Attardi | N/A |
| Mouse: E1A;HRasG12V p53−/− MEFs | Laboratory of Dr. Laura Attardi | N/A |
| Mouse: E1A;HRasG12V p53WT MEFs shLuc | This paper | N/A |
| Mouse: E1A;HRasG12V p53WT MEFs shMettl3-1 | This paper | N/A |
| Mouse: E1A;HRasG12V p53WT MEFs shMettl3-2 | This paper | N/A |
| Mouse: E1A;HRasG12V p53−/− MEFs shLuc | This paper | N/A |
| Mouse: E1A;HRasG12V p53−/− MEFs shMettl3-1 | This paper | N/A |
| Mouse: E1A;HRasG12V p53−/− MEFs shMettl3-2 | This paper | N/A |
| Mouse: Flp-In™-3T3 | Thermo Fisher | R76107 |
| Mouse: Flp-In-3T3 p53-LAP | This paper | N/A |
| Mouse: Flp-In-3T3 p53−/− | This paper | N/A |
| Mouse: Embryonic Stem cells Wild-type | Laboratory of Dr. Howard Y. Chang | N/A |
| Mouse: Embryonic Stem cells Mettl3−/− | Laboratory of Dr. Howard Y. Chang | N/A |
| Human: A549 lung cancer cell line: TP53WT | Stanford University School of Medicine laboratories | N/A |
| Human: A549 lung cancer cell line: TP53−/− | This manuscript | N/A |
| Human: H1299 lung cancer cell line | Stanford University School of Medicine laboratories | N/A |
| Experimental models: Organisms/strains | ||
| Mouse: ICR-Scid: IcrTac:ICR-Prkdcscid | Taconic Biosciences | ICRSC-M |
| Mouse: KrasLSL-G12D mice: B6.129S4-Krastm4Tyj/J | Laboratory of Dr. Tyler Jacks | N/A |
| Mouse: Rosa26LSL-tdTomato | Madisen et al. (2010) | N/A |
| Mouse: H11LSL-Cas9: B6;129-Igs2tm1(CAG-cas9+)Mmw/J | Chiou et al. (2015); Laboratory of Dr. Monte Winslow | 026816 |
| Mouse: Mettl14fl/fl | Wang et al. (2018); Stanford University School of Medicine laboratories | N/A |
| Oligonucleotides | ||
| See Table S4 for primers | This paper | N/A |
| Recombinant DNA | ||
| pENTR p53 | This paper | N/A |
| pG-LAP7/puro destination vector | Laboratory of Dr. Peter Jackson | N/A |
| pG-LAP7/puro p53 (p53-LAP) | This paper | N/A |
| pENTR Mettl3 | This paper | N/A |
| pG-LAP2 Mettl3WT (FLAG-METTL3 WT) | This paper | N/A |
| pG-LAP2 Mettl3APPA (FLAG-METTL3 APPA) | This paper | N/A |
| pCS2-HA destination vector | Laboratory of Dr. Peter Jackson | N/A |
| pCS2-HA-Mettl3 (HA-METTL3) | This paper | N/A |
| pcDNA3.1–3XHA-p53 | Laboratory of Dr. Laura Attardi | N/A |
| pcDNA3.1–3XHA-p53 Δ1–42 | This paper | N/A |
| pcDNA3.1–3XHA-p53 Δ1–61 | This paper | N/A |
| pX330 p53 | Addgene | 59910 |
| shRNA vectors with shRNAs targeting Luciferase, Mettl3, METTL3 | Laboratory of Dr. Pedro Batista | N/A |
| Lenti-U6-sgMettl3 | This paper | N/A |
| Lenti-U6-sgNeoR1 | Laboratory of Dr. Monte Winslow | N/A |
| pX458 TP53 series | This paper | N/A |
| Software and algorithms | ||
| Enrichr | Chen et al. (2013), Kuleshov et al. (2016) | https://maayanlab.cloud/Enrichr/ |
| Metascape | Zhou et al. (2019) | http://metascape.org/gp/index.html#/main/step1 |
| Byonic | Protein Metrics | https://proteinmetrics.com/resources/byonic-advanced-peptide-and-protein-identification-software/ |
| Image Lab | Bio-Rad | https://www.bio-rad.com/en-us/product/image-lab-software?ID=KRE6P5E8Z |
| NDPview 2.0 | Hamamatsu | https://www.hamamatsu.com/us/en/product/type/U12388-01/index.html |
| QPath | Univ of Edinburgh | https://qupath.github.io/ |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| Umi_tools (v0.5.1) | Smith et al. (2017) | https://github.com/CGATOxford/UMI-tools |
| Cutadapt (v2.7) | Martin (2011) | https://github.com/marcelm/cutadapt |
| STAR (v2.6.0c) | Dobin et al. (2013) | https://github.com/alexdobin/STAR |
| CLIPper | Lovci et al. (2013) | https://github.com/YeoLab/clipper |
| GENCODE (release M21) | Frankish et al. (2019) | https://www.gencodegenes.org/human/ |
| HOMER (v3.1) | Heinz et al. (2010) | http://homer.ucsd.edu/homer/motif/motifDatabase.html |
| limma (v3.46) | Ritchie et al. (2015) | https://bioconductor.org/packages/release/bioc/html/limma.html |
| genefu (v2.22.1) | Gendoo et al. (2016) | http://bioconductor.org/packages/release/bioc/html/genefu.html |
| DISCOVER package | Canisius et al. (2016) | https://ccb.nki.nl/software/discover/ |
| DEseq2 | Love et al. (2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Fastp | Chen et al. (2018) | https://github.com/OpenGene/fastp |
| Featurecounts (1.5.3) | Liao et al. (2014) | https://rnnh.github.io/bioinfo-notebook/docs/featureCounts.html |