KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-H3K9me1 | Abcam | Cat#ab176880; RRID#AB_2751009 |
| Rabbit polyclonal anti-H3K9me3 | Abcam | Cat#ab8898; RRID#AB_306848 |
| Rabbit polyclonal anti-Histone H3 | Abcam | Cat#ab46765; RRID#AB_880439 |
| Rabbit monoclonal anti-alpha Tubulin | Cell Signaling Technologies | Cat#cst2125; RRID#AB_2619646 |
| IRDye® 800CW Goat anti-Rabbit | LI-COR Biosciences | Cat#925-32211; RRID#AB_2651127 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| UNC0642 G9a/GLP Inhibitor | R&D Systems | Cat#5132/10 |
| DNA Degradase Plus | Zymo Research | Cat#E2020 |
| Lipofectamine RNAiMax | Thermo Fisher | Cat#13778030 |
| L-Lysine-2HCl | Thermo Fisher Scientific | Cat#PI89987 |
| L-Arginine-HCl 13C6 15N4 | Thermo Fisher | Cat#PI89990 |
| Dimethyl Sulfoxide (DMSO) | Sant Cruz Biotechnology | Cat#sc-358801 |
| Sequencing Grade Modified Trypsin | Promega | Cat#V5113 |
| Propionic Anhydride | Sigma-Aldrich | Cat#240311 |
| Phenyl Isocyanate | Sigma-Aldrich | Cat#78750-25ML |
| Leupeptin Hemisulfate | Thermo Fisher | Cat#AAJ61188MC |
| Aprotinin | Gold Biotechnology | Cat#A-655-100 |
| Phenylmethylsulfonyl Fluoride (PMSF) | Gold Biotechnology | Cat#P-470-50 |
| Trichostatin A | Thermo Fisher | Cat#501012404 |
| Sodium Butyrate | Sigma-Aldrich | Cat#303410-100G |
| Nicotinamide | Sigma-Aldrich | Cat#N3376-500G |
| Urea | Acros Organics | Cat#197460050 |
| Dithiothreitol (DTT) | Gold Biotechnology | Cat#DTT100 |
| Iodoacetamide | Sigma-Aldrich | Cat#I1149-5G |
| Ammonium Bicarbonate | Sigma-Aldrich | Cat#09830-500G |
| Micrococcal Nuclease (MNase) | Worthington Biochemical | Cat#LS004798 |
| Proteinase K | Thermo Fisher | Cat#EO0491 |
| TRIzol™ | Thermo Fisher | Cat#15596018 |
| TRI Reagent | Sigma-Aldrich | Cat#T9424-25ML |
| 3M Empore C18 47mm extraction disks | Empore | Cat#2215 |
| Atlantis dC18 NanoEase Column (3 μM, 100 μM, 150 mm) | Waters | Cat#186002209 |
| XBridge BEH Amide Column (3.5 μM, 2.1 mm, 150mm) | Waters | Cat#186004860 |
| Superscript III Reverse Transcriptase | Thermo Fisher | Cat#18080044 |
| RPMI-1640 | Thermo Fisher | Cat#11875119 |
| RPMI-1640 for SILAC | Thermo Fisher | Cat#88365 |
| RPMI-1640, no methionine | Thermo Fisher | Cat#A1451701 |
| Fetal Bovine Serum (FBS) | Thermo Fisher | Cat#16000044 |
| Dialyzed Fetal Bovine Serum (DFBS) | Thermo Fisher | Cat#88212 |
| H3K9 unmodified peptide | This paper | N/A |
| pET28a-LIC-4H4H | Addgene | Plasmid # 51314; RRID#Addgene_51314 |
| pET28a-LIC-EHMT2-913-1193 | Peter W. Lewis Laboratory | N/A |
| Critical Commercial Assays | ||
| PerfeCTa SYBR® Green SuperMix | Quanta Bio | Cat#95054-02K |
| SYBR Green PCR Master Mix | Thermo Fisher | Cat#4309155 |
| REVERT Total Protein Stain | LI-COR Biosciences | Cat#926-11011 |
| RevertAid First Strand cDNA Synthesis Kit | Thermo Fisher | Cat#K1621 |
| Wizard® Genomic DNA Purification Kit | Promega | Cat#A1120 |
| Dynabeads™ M-280 Sheep Anti Rabbit IgG | Thermo Fisher | Cat#11203D |
| QIAquick PCR Purification Kit | QIAGEN | Cat#28104 |
| TruSeq DNA Nano | Illumina | Cat#20015964 |
| Axygen™ Light Cycler 480 Compatible PCR Plates | Thermo Fisher | Cat#14-223-212 |
| Promega MTase-Glo™ | Promega | Cat#V7602 |
| Deposited Data | ||
| H3K9me1 and H3K9me3 ChIP-sequencing Data | This paper | GEO Accession Number: GSE122565 |
| RNA-sequencing Data | This paper | GEO Accession Number: GSE138574 |
| Experimental Models: Cell Lines | ||
| H. sapiens: HCT116 | ATCC | CCL-247 |
| H. sapiens: HEK-293T | ATCC | CRL-3216 |
| H. sapiens: HEK-293 | ATCC | CRL-1573 |
| H. sapiens: HepG2 | ATCC | HB-8065 |
| H. sapiens: MCF7 | ATCC | HTB-22 |
| H. sapiens: Panc1 | ATCC | CRL-1469 |
| M. musculus: Hepa-1c1c7 | ATCC | CRL-2026 |
| Experimental Models: Organisms/Strains | ||
| M. musculus: C57BL/6J (9-weeks of age) | The Jackson Laboratory | JAX: 000664 |
| M. musculus: C57BL/6J (2- and 18-months of age) | The National Institute on Aging Rodent Colony | N/A |
| Oligonucleotides | ||
| 5-Methylcytosine and 5-Hydroxymethylcytosine DNA | Zymo Research | Cat#D505 |
| Stealth RNAi Sense Sequence: H. sapiens MAT2A: 5′AUCAAGGACAGCAUCACUGAUUUGG-3′ | Thermo Fisher | Kera et al., 2013 |
| Stealth RNAi Sense Sequence: Control: 5′-AGGAGGAUAUUACCAUGGACAAGAC-3′ | Thermo Fisher | Kera et al., 2013 |
| SUV39H1 RNAi: H. sapiens | Novus Biologicals | H00006839-R01-20nmol |
| SUV39H2 RNAi: H. sapiens | Novus Biologicals | H00079723-R01-20nmol |
| SETDB1 RNAi: H. sapiens | Novus Biologicals | H00009869-R01-20nmol |
| G9a/EHMT2 RNAi: H. sapiens | Novus Biologicals | H00010919-R02-20nmol |
| GLP/EHMT1 RNAi: H sapiens | Novus Biologicals | H00079813-R01-20nmol |
| RT-qPCR Primers | See Table S2 | See Table S2 |
| Software and Algorithms | ||
| Bowtie2-2.1.0 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Samtools 1.5 | Li et al., 2009 | http://samtools.sourceforge.net/ |
| MACS2-2.1.1.20160309 | Zhang et al., 2008 | http://liulab.dfci.harvard.edu/MACS/ |
| Bedtools v2.25.0 | Quinlan and Hall, 2010 | https://bedtools.readthedocs.io/en/latest/ |
| HOMER v4.9 | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ |
| GelAnalyzer 2010a | Lazar Software | http://gelanalyzer.com/index.html |
| MAVEN | Melamud et al., 2010; Clasquin et al., 2012 | http://genomics-pubs.princeton.edu/mzroll/index.php |
| MAXQUANT | Cox et al., 2014 | http://www.biochem.mpg.de/5111795/maxquant |
| Trimmomatic v0.39 | Bolger et al., 2014 | http://www.usadellab.org/cms/?page=trimmomatic |
| RSEM v1.2.4 | Li et al., 2011 | https://deweylab.github.io/RSEM/ |
| EBSeq v1.24.0 | Leng et al., 2013 | http://bioconductor.org/packages/release/bioc/html/EBSeq.html |
| GSEA 2 | Tamayo et al., 2005 Mootha et al., 2003 |
http://software.broadinstitute.org/gsea/index.jsp |
| Skyline | MacLean et al., 2010 | https://skyline.ms/project/home/software/Skyline/begin.view |
| Other | ||
| Control M. musculus Diet | Envigo | TD.01084 |
| Methionine Deficient M. musculus Diet | Envigo | TD.140119 |