KEY RESOURCE TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-c-MYC (clone 9E10) | Santa Cruz Biotechnology | Cat#sc-40, ProSci Cat#51-118, RRID:AB_1947601 |
| Rabbit polyclonal anti-D2HGDH | Proteintech | Cat#13895-1-AP, RRID:AB_2089330 |
| Rabbit polyclonal anti-L2HGDH | Proteintech | Cat#15707-1-AP, RRID:AB_2133202 |
| Mouse polyclonal anti-ALKBH5 | Abcam | Cat#ab69325, RRID:AB_1267666 |
| Mouse monoclonal anti-FTO - Fatso (C-3) | Santa Cruz Biotechnology | Cat#sc-271713, RRID:AB_10707817 |
| Mouse monoclonal anti-m6A | Synaptic System | Cat#202003, RRID:AB_2279214 |
| Mouse monoclonal anti-TET1 (Clone GT1462) | Sigma-Aldrich | Cat#SAB2700730 |
| Rabbit monoclonal anti-TET2 | Cell Signaling Technology | Cat#18950, RRID:AB_2798809 |
| Rabbit polyclonal anti-TET3 | EMD Millipore Corporation | Cat#ABS463 |
| Rabbit polyclonal anti-TET3 | Sigma-Aldrich | Cat#HPA050845; RRID:AB_2681256 |
| Rabbit monoclonal anti-METTL3 (Clone D2I6O) | Cell Signaling Technology | Cat#96391; RRID:AB_2800261 |
| Rabbit monoclonal anti-METTL14 (Clone D8K8W) | Cell Signaling Technology | Cat#51104, RRID:AB_2799383 |
| Rabbit polyclonal anti-WTAP | Cell Signaling Technology | Cat#56501, RRID:AB_2799512 |
| Rabbit monoclonal anti-5-Methylcytosine (Clone D3S2Z) | Cell Signaling Technology | Cat#28692, RRID:AB_2798962 |
| Mouse monoclonal anti-5-hydroxymethylcytosine (Clone HMC31) | Cell Signaling Technology | Cat#51660, RRID:AB_2799398 |
| Mouse monoclonal anti-β-actin (clone AC-74) | Sigma-Aldrich | Cat#A2228, RRID:AB_476697 |
| Mouse monoclonal anti-FLAG (Clone M2) | Sigma-Aldrich | Cat#F3165, RRID:AB_259529 |
| Rabbit polyclonal anti-Lamin A | Bethyl Laboratories | Cat#A303-433A-M, RRID:AB_10951693 |
| Mouse monoclonal anti-Tubulin (Clone DM1A) | Thermo-Fisher | Cat# 62204, RRID:AB_1965960 |
| Normal mouse IgG | Santa Cruz Biotechnology | Cat#sc-2025, RRID:AB_737182 |
| Donkey anti-mouse IgG Alexa Fluor 488 | Thermo-Fisher | Cat#A-21202; RRID:AB_141607 |
| Donkey Anti-rabbit IgG Alexa Fluor 568 | Thermo-Fisher | Cat#A-10042, RRID:AB_2534017 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Dimethyl 2-oxoglutarate | Sigma-Aldrich | Cat#349631, CAS: 13192-04-6 |
| Octyl-D-2-HG | Toronto Research Chemicals | Cat#H942595, CAS:1391068-16-8 |
| Octyl-L-2-HG | Toronto Research Chemicals | Cat#H942596, CAS: 1391067-96-1 |
| Dimethyloxalylglycine (DMOG) | Frontier Scientific | Cat#D1070, CAS: 89464-63-1 |
| CB-839 | Cayman Chemical | Cat#2203 |
| Dimethyl sulfoxide | Sigma-Aldrich | Cat#D8418, CAS: 67-68-5 |
| Tetracycline | Sigma-Aldrich | Cat#T-7660, CAS: 64-75-5 |
| Glycine | Thermo-Fisher Scientific | Cat#BP381-5, CAS: 56-40-6 |
| Formaldehyde | Thermo-Fisher Scientific | Cat#28908, CAS: 50-00-0 |
| Dynabeads protein G | Invitrogen | Cat#10003D |
| OneMinute Western Blot Stripping Buffer | GM Biosciences | Cat#GM6001 |
| 4,6-diamidino-2-phenylindole - DAPI | Sigma-Aldrich | Cat#D9542, CAS: 28718-90-3 |
| Trizol | Life technologies | Cat#15596018, CAS: 108-95-2 (Phenol), CAS: 593-84-0 (Guanidine isothiocyanate), CAS: 1762-95-4 (Ammonium thiocyanate). |
| Critical Commercial Assays | ||
| 5mC-Hydroxylase TET Activity Assay Kit | Epigentek | Cat#P-3086 |
| m6A Demethylase Activity Kit | Epigentek | Cat#P-9013 |
| Methylated DNA (5mC) Quantification Kit | Epigentek | Cat#P-1034 |
| Hydroxymethylated DNA (5hmC) Quantification Kit | Epigentek | Cat#P-1036 |
| EpiQuik™ m6A RNA Methylation Quantification Kit | Epigentek | Cat#P-9005 |
| EpiQuik Nuclear Extraction Kit I | Epigentek | Cat#OP-0002 |
| Gentra Puregene DNA purification kit | Qiagen | Cat#158667 |
| Luciferase Assay Systems | Promega | Cat#E1500 |
| β-Galactosidase Enzyme Assay System | Promega | Cat#E2000 |
| Lipofectamine 2000 | Thermo-Fisher | Cat#11668-019 |
| Mouse B Cell Isolation | Stemcell Technologies Inc | Cat#19854 |
| High Capacity cDNA Reverse Transcription Kit | Applied Biosystems | Cat#4368814 |
| Amicon Ultra Centrifugal Filters-10K | Millipore | Cat#UFC501096 |
| Experimental Models: Cell Lines | ||
| SU-DHL8 | ATCC | CRL-2961 |
| SU-DHL10 | ATCC | CRL-2963 |
| OCI-Ly1 | DSMZ | ACC-722 |
| OCI-Ly3 | DSMZ | ACC-761 |
| OCI-Ly8 | Cellosaurus | CVCL_8803 |
| OCI-Ly10 | Cellosaurus | CVCL_8795 |
| Pfeiffer | ATCC | CRL-2632 |
| U2932 | DSMZ | ACC-633 |
| HS-Sultan | ATCC | CRL-1484 |
| P493-6 | Cellosaurus | CVCL_6783 |
| HEK-293 | ATCC | CRL-1573 |
| HEK-293FT | Invitrogen | R70007 |
| Experimental Models: Organisms/Strains | ||
| C57BL/6 mice | Charles River | Strain code: 027 |
| B6.Cg-Tg(IghMyc)22Bri/J | The Jackson laboratory | Stock number: 002728 |
| Oligonucleotides | ||
| Primers for PCR, see Table S2 | This paper | N/A |
| ShRNA and guide RNA, see Table S2 | This paper | N/A |
| Recombinant DNA | ||
| pGL3-basic vector | Promega | Cat# 1751 |
| pCDNA3-FLAG-MYC | gift from Dr. Yuzuru Shiio | N/A |
| pLCRISPR.EFS.GFP | Heckl et al., 2014 | Addgene plasmid #57818 |
| lentiCRISPR v2 | Sanjana et al., 2014 | Addgene plasmid #52961 |
| FH-TET3-pEF | Ko et al., 2013 | Addgene plasmid #49446 |
| Tet-pLKO-puro | Wiederschain et al., 2009 | Addgene plasmid #21915 |
| PAX2 | unpublished | Addgene plasmid #12260 |
| pMD2.G | unpublished | Addgene plasmid #12259 |
| pCMVβ-gal | Clontech | Cat# PT2004-5 |
| p3XFLAG-CMV | Sigma-Aldrich | Cat# E7658 |
| Software and Algorithms | ||
| Prism Software | GraphPad Software Inc | version 5.02 and 8.2.0 |
| UCSC genome browser | Public website | https://genome.ucsc.edu |
| The Cancer Genome Atlas (TCGA) program | Broad firehose - version 2016_01_28 | https://gdac.broadinstitute.org/ |
| GISTIC2.0 algorithm | Mermel et al. 2011 (PMID 21527027) | ftp://ftp.broadinstitute.org/pub/GISTIC2.0/all_versions |
| MatInspector | Genomatix | https://www.genomatix.de/downloads.html |
| Others | ||
| 35mm glass bottom microwell dishes | MatTek Corporation | P35GCOL-1.5-14-C |
| Nylon membrane - Hybond-N | GE Healthcare | Cat # RPN82N |
| HPLC Zorbax Eclipse Plus C18 RRHD | Agilent | Cat# 959996-902 |
| Pan-Cancer Atlas | Hutter and Zenklusen, 2018 (PMID 29625045) | https://gdc.cancer.gov/node/905/ |
| TCGA DLBCL dataset | Schmitz et al. 2018 (PMID 29641966) | http://gdac.broadinstitute.org/ |
| Enhancer coordinates | Chapuy et al. 2013 (PMID 24332044) | Table S7; https://www.sciencedirect.com/science/article/pii/S1535610813004911?via%3Dihub |