KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-5-methylcytosine Antibody, clone 33D3 | Millipore Sigma | Cat# MABE146; RRID:AB_10863148 |
| anti-TurboGFP | Thermo Fisher Scientific | Cat# PA5–22688; RRID:AB_2540616 |
| Anti-p53 antibody, Mouse monoclonal (clone DO-1) | Sigma Aldrich | Cat# P6874; RRID:AB_1079545 |
| p53 (1C12) Mouse mAb | Cell Signaling | Cat# 2524; RRID:AB_331743 |
| beta Tubulin antibody | GeneTex | Cat# GTX101279; RRID:AB_1952434 |
| Anti-Actin Antibody, clone C4 | Millipore Sigma | Cat# MAB1501; RRID:AB_2223041 |
| IRDye® 800CW Goat anti-Mouse IgG Secondary Antibody | Li-Cor | Cat# 926–32210; RRID:AB_621842 |
| IRDye® 680LT Goat anti-Rabbit IgG Secondary Antibody | Li-Cor | Cat# 926–68021; RRID:AB_10706309 |
| Bacterial and virus strains | ||
| One Shot® Mach1 T1 Phage-Resistant Chemically Competent E. coli | Invitrogen | C862003 |
| Chemicals, peptides, and recombinant proteins | ||
| DMEM high glucose | MSKCC Media Core | N/A |
| Fetal Bovine Serum | VWR | Cat# 97068–085 |
| Penicillin-Streptomycin | MSKCC Media Core | N/A |
| RPMI 1640 Medium | ThermoFisher Scientific | Cat# 11875093 |
| 2-mercaptoethanol | GIBCO | ThermoFisher Scientific cat# 21985023 |
| L-Asparagine | Sigma-Aldrich | Cat# A4159 |
| Purelink Genomic DNA Mini Kit | Invitrogen | Cat# K182002 |
| Brilliant II QRT-PCR SYBR® Green Low ROX Master Mix | Agilent Technologies | Cat# 600835 |
| Pan B Cell Isolation Kit II | Miltenyi Biotec | Cat# 130-104-443 |
| MACS BSA Stock Solution | Miltenyi Biotec | Cat# 130-091-376 |
| autoMACS Rinsing Solution | Miltenyi Biotec | Cat# 130-091-222 |
| MACS LS Columns | Miltenyi Biotec | Cat# 130-042-401 |
| RNeasy Plus Mini Kit | QIAGEN | Cat# 74136 |
| Phusion HF PCR Master Mix | NEB | Cat# M0531 |
| BamHI | NEB | Cat# R0136 |
| NotI-HF | NEB | Cat# R3189 |
| AarI | Thermo Scientific | Cat# ER1581 |
| Rapid DNA Dephos & Ligation Kit | Sigma-Aldrich | Cat# 4898117001 |
| Lenti-X Packaging Single Shots | Takara | Cat# 631282 |
| Lenti-X Concentrator | Takara | Cat# 631231 |
| Calphos Mammalian Transfection Kit | Clontech | Cat# 631312 |
| Puromycin 10mg/ml | Invivogen | Cat# ant-pr-1 |
| Hygromycin B (50 mg/mL) | ThermoFisher Scientific | Cat# 10687010 |
| Methanol | Fisher Scientific | Cat# A412P-4 |
| Crystal violet solution | Sigma-Aldrich | Cat# HT90132 |
| Nutlin-3 | Sigma-Aldrich | Cat# N6287 |
| DMSO | Fisher Scientific | Cat# BP231–100 |
| DAPI Staining Solution | Miltenyi Biotec | Cat# 130-111-570 |
| Dynabeada Protein G for Immunoprecipitation | Thermo Fisher Scientific | Cat# 10003D |
| Proteinase K | Thermo Fisher Scientific | Cat# AM2548 |
| Phenol:Chloroform Saturated Solution, Ph 6.7. ≥ 99.0% | MP Biomedicals | Cat# ICNA04802521 |
| 3M Sodium Acetate | Ambion | Cat# AM9740 |
| GlycoBlue | Ambion | Cat# AM9516 |
| 5-Aza-2-deoxycytidine | Sigma-Aldrich | Cat# A3656 |
| PureLink RNase A (20 mg/mL) | Fisher Scientific | Cat# 12091021 |
| EpiMark® Bisulfite Conversion Kit | New England Biolabs | Cat# E3318S |
| EpiMark® Hot Start Taq DNA Polymerase | New England Biolabs | Cat# M0490 |
| Cycloheximide | Sigma-Aldrich | Cat# C4859 |
| Bolt 4 to 12%, Bis-Tris, 1.0 mm Mini Protein Gel, 12-well | Thermo Fisher Scientific | Cat# NW04122BOX |
| 20X Bolt MOPS SDS Running Buffer | Thermo Fisher Scientific | Cat# B0001 |
| Invitrogen novex NuPAGE 4–12% Bis-Tris Midi Protein Gels, 20 well | Thermo Fisher Scientific | Cat# WG1402BOX |
| Bolt Transfer Buffer (20X) | Thermo Fisher Scientific | Cat# BT00061 |
| Nitrocellulose Membrane, 0.45 mm | BioRad | Cat# 1620115 |
| Revert 700 Total Protein Stain Kits for Western Blot Normalization | Li-Cor | Cat# 926–11010 |
| Critical commercial assays | ||
| Click-iT® Plus EdU Alexa Fluor® 488 Flow Cytometry Assay Kit | ThermoFisher Scientific | Cat# C10632 |
| ApoStat Apoptosis Detection Kit | R&D Systems | Cat# FMK012 |
| Qubit Protein Assay Kit | Invitrogen | Cat# Q33212 |
| Deposited data | ||
| Benign Adipose Methylation Array | Benton et al., 2015 | EMBL-EBI: E-MTAB-1866 |
| Benign Glia Methylation Array | Do et al., 2016 | GEO: GSE79144 |
| Benign Melanocyte Methylation | Fujiwara et al., 2019 | GEO: GSE122909 |
| Benign Melanocyte Methylation | Marzese et al., 2014 | GEO: GSE44662 |
| Experimental models: cell lines | ||
| Human: BJ Fibroblasts | ATCC | ATCC Cat# CRL-2522; RRID:CVCL_3653 |
| Human: HT-1080 | ATCC | ATCC Cat# CRL-7951; RRID:CVCL_0317 |
| Human: LentiX-293T | Takara | Cat# 632180 |
| Human: Pheonix-293T | Nolan Laboratory, Stanford University | N/A |
| Mouse Embryonic Fibroblasts | This paper | N/A |
| Mouse: Em-myc lymphoma cell lines | This paper | N/A |
| Experimental models: organisms/strains | ||
| Mouse: C57BL/6-Dinoegfp | Howard Chang, Stanford University | N/A |
| Mouse: C57BL/6 Eμ-myc | Scott Lowe, MSKCC | N/A |
| Mouse: C57BL/6 Cdkn1a−/− (B6.129S6(Cg)-Cdkn1atm1Led/J) | Jackson Labs | IMSR Cat# JAX:016565;RRID:IMSR_JAX:016565 |
| Mouse: CB17-Prkdc< scid > | Taconic | IMSR Cat# TAC:cb17sc; RRID:IMSR_TAC:cb17sc |
| Mouse: C57BL/6 | Jackson Labs | IMSR Cat# JAX:000664; RRID:IMSR_JAX:000664 |
| Oligonucleotides | ||
| PCR Primers | This paper (see Table S4) | N/A |
| Recombinant DNA | ||
| Plasmid: pCDH-EF1α-MCS-(PGK-GFP-T2A-Puro) | System Biosciences | Cat# CD813A-1 |
| Plasmid: pCDH-EF1α-Dino-(PGK-GFP-T2A-Puro) | This paper | N/A |
| Plasmid: pMSCV-IRES-mCherry FP | Addgene | RRID:Addgene_52114 |
| Plasmid: pBabe 12S E1A | Addgene | RRID:Addgene_18742 |
| Plasmid: pWZL hygro H-RasV12 | Addgene | RRID:Addgene_18749 |
| Plasmid: Fuw-dCas9-Tet1CD-P2A-BFP | Addgene | RRID:Addgene_108245 |
| Plasmid: Fuw-dCas9-dead Tet1CD-P2A-BFP | Addgene | RRID:Addgene_108246 |
| Plasmid: pgRNA-modified | Addgene | RRID:Addgene_84477 |
| Plasmid: pgRNA-modified_sgDINO | This paper | N/A |
| Software and algorithms | ||
| R | (R Core Team, 2020) | |
| featureCounts | CRAN | Liao et al., 2014 |
| DESeq2 | CRAN | Love et al., 2014 |
| XLSTAT | Addinsoft | N/A |
| Prism | GraphPad | v8 |
| ImageJ | NIH | Schneider et al., 2012 |
| FlowJo | BD Biosciences | N/A |
| FCS Express | De Novo Software | V6 |
| Custom Alt-R® CRISPR-Cas9 guide RNA tool | Integrated DNA Technologies | https://www.idtdna.com/site/order/designtool/index/CRISPR_CUSTOM |
| Image Studio | Li-Cor | N/A |
| Other | ||
| QuantStudio 6 Flex Real-Time PCR system | Applied Biosytems | N/A |
| MACS Multistand | Miltenyi Biotec | Cat# 130-042-303 |
| MidiMACS Separator | Miltenyi Biotec | Cat# 130-042-302 |
| LSR Fortessa | BD Biosciences | N/A |
| FACSAria | BD Biosciences | N/A |
| Biorupter Pico | Diagenode | B01060010 |
| Qubit 3.0 Fluorometer | Invitrogen | Cat# Q33216 |
| Odyssey CLx Imaging System | Li-Cor | Model# 9140 |