KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| H3K27ac | Abcam | Cat# ab4729, RRID: AB_2118291 |
| H3K27me3 | Abcam | Cat# ab6002, RRID:AB_305237 |
| H3K4me1 | Cell Signaling Technology | Cat# 5326, RRID:AB_10695148 |
| H3K4me3 | Abcam | Cat# ab8580, RRID:AB_306649 |
| H3 | Abcam | Cat# ab1791, RRID:AB_302613 |
| TTF-1 | Seven Hills Bioreagents (WRAB-1231) | Cat# WRAB-1231 RRID: AB_451727 |
| Ki-67 | Cell Signaling Technology | Cat# 9027, RRID:AB_2636984 |
| ENO1 | Abcam (ab227978) | Cat# ab227978 RRID: |
| PGK1 | Abcam | Cat# ab38007, RRID:AB_2161220 |
| PGAM1 | Novus | Cat# NBP1-49532, RRID:AB_10011581 |
| TTF-1 | Abcam | Cat# ab72876, RRID:AB_1271363 |
| KMT2D | Santa Cruz Biotechnology | Cat# sc-68675, RRID:AB_2145784 |
| Actin | Sigma-Aldrich | Cat# A5441, RRID:AB_476744 |
| HRP-conjugated anti-mouse-IgG | Santa Cruz Biotechnology | Cat# sc-2055, RRID:AB_631738 |
| HRP-conjugated anti-rabbit-IgG | Santa Cruz Biotechnology (sc-2004) | Cat# sc-2004, RRID:AB_631746 |
| Alexa 488-conjugated anti-mouse IgG | Life technologies (A11029) | Cat# A-11029, RRID:AB_138404 |
| Alexa 488-conjugated anti-rabbit IgG | Life technologies (A11037) | Cat# A-11037, RRID:AB_2534095 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| 2-Deoxy-D-glucose (2-DG) | Selleck Chemicals | Cat# S4701; CAS: 1032350-13-2 |
| Vorinostat (SAHA, MK0683) | Selleck Chemicals | Cat# S1047; CAS: 149647-78-9 |
| AR-42 (HDAC-42) | Selleck Chemicals | Cat# S2244; CAS: 935881-37-1 |
| Lonidamine | Selleck Chemicals | Cat# S2610; CAS: 50264-69-2 |
| Dinaciclib | Selleck Chemicals | Cat# S2768; CAS: 779353-01-4 |
| Koningic acid (KA) | Focus Biomolecule | Cat# 10-3326; CAS: 74310-84-2 |
| IACS-010759 | Gift from Dr. Joseph R. Marszalek (Molina et al., 2018) | N/A |
| Critical Commercial Assays | ||
| Seahorse XF Glycolysis stress test kit | Agilent | Cat# 103020-100 |
| Seahorse XF Cell Mito stress test kit | Agilent | Cat# 103015-100 |
| Glyceraldehyde 3 Phosphate Dehydrogenase Activity Assay Kit | Abcam | Cat# ab204732 |
| Enolase Assays Kit | Abcam | Cat# ab241024 |
| Deposited Data | ||
| RNA-seq for KrasLSL-G12D and KrasLSL-G12D;Kmt2dfl/fl lung tumors | This paper | GEO: GSE116658 |
| ChIP-seq for KrasLSL-G12D and KrasLSL-G12D;Kmt2dfl/fl lung tumors | This paper | GEO: GSE116659 |
| RNA-seq for LKR10 lung cancer cell line | This paper | GEO: GSE143498 |
| Experimental Models: Cell Lines | ||
| Human: NCI-A549 | ATCC | CCL-185 |
| Human: NCI-H1792 | ATCC | CRL-5895 |
| Human: NCI-H23 | ATCC | CRL-5800 |
| Human: NCI-H1437 | ATCC | CRL-5872 |
| Human: NCI-H358 | ATCC | CRL-5807 |
| Human: NCI-H1568 | ATCC | CRL-5876 |
| Human: DV-90 | DSMZ | ACC 307 |
| Human: CORL-105 | ECACC | 92031918 |
| Mouse: LKR-10 | Gift from Julien Sage | N/A |
| Experimental Models: Organisms/Strains | ||
| Mouse: B6.129-Krastm4Tyj/Nci, | NCI Mouse Repository | Strain: 01XJ6 |
| Mouse: B6.129P2-Trp53tm1Brn/J | The Jackson Laboratory | Strain: 008462 |
| Mouse: Kmt2dfl/fl (also called Mll4fl/fl) | (Dhar et al., 2018) | N/A |
| Oligonucleotides | ||
| Primers for quantitative RT-PCR (mouse): See Table S4 | N/A | N/A |
| Primers for quantitative RT-PCR for enhancer RNAs: See Table S4 | N/A | N/A |
| Primers for genotyping: See Table S4 | N/A | N/A |
| Primers for quantitative ChIP-PCR (mouse): See Table S4 | N/A | N/A |
| Primers for cloning: See Table S4 | N/A | N/A |
| Recombinant DNA | ||
| pInducer20-KMT2D | This paper | N/A |
| shKmt2d-01 (mouse) | Sigma-Aldrich | Cat# TRCN0000239234 |
| shKmt2d-03 (mouse) | Sigma-Aldrich | Cat# TRCN0000239233 |
| shPer2-01 (mouse) | Sigma-Aldrich | Cat# TRCN0000284505 |
| shPer2-02(mouse) | Sigma-Aldrich | Cat# TRCN0000096663 |
| Software and Algorithms | ||
| ImageJ | (Schneider et al., 2012) | https://imagej.nih.gov/ij/ |
| cBio cancer genomics portal | (Cerami et al., 2012; Gao et al., 2013) | http://www.cbioportal.org |
| IBM SPSS Statistics 23 | IBM | https://www.ibm.com/support/pages/downloading-ibm-spss-statistics-23 |
| Pyflow-ChIPseq | (Terranova et al., 2018) | https://github.com/crazyhottommy/pyflow-ChIPseq |
| Bowtie1 | (Langmead et al., 2009) | http://bowtie-bio.sourceforge.net/index.shtml |
| samtools | (Li et al., 2009) | http://www.htslib.org/ |
| Deeptools | (Ramirez et al., 2016) | https://deeptools.readthedocs.io/ |
| MACS14 | (Zhang et al., 2008) | https://github.com/taoliu/MACS |
| ROSE | (Whyte et al., 2013) | http://younglab.wi.mit.edu/super_enhancer_code.html |
| chromHMM | (Ernst and Kellis, 2012) | http://compbio.mit.edu/ChromHMM/ |
| Epilogos | (Marx, 2015) | https://github.com/Altius/epilogos |
| EnrichedHeatmap | (Gu et al., 2018) | https://bioconductor.org/packages/release/bioc/html/EnrichedHeatmap.html |
| ComplexHeatmap | (Gu et al., 2016) | https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html |
| STAR | (Dobin et al., 2013) | https://github.com/alexdobin/STAR |
| featureCounts | (Liao et al., 2014) | http://subread.sourceforge.net/ |
| ChIPseeker | (Yu et al., 2015) | https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html |
| DESeq2 | (Love et al., 2014) | http://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| TCGAbiolinks | (Colaprico et al., 2016) | https://bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html |
| KaryoploteR | (Gel and Serra, 2017) | http://bioconductor.org/packages/release/bioc/html/karyoploteR.html |
| GSEA | (Subramanian et al., 2005) | http://software.broadinstitute.org/gsea/ |
| Snakemake | (Koster and Rahmann, 2012) | https://snakemake.readthedocs.io/en/stable/ |
| Pyflow-RNAseq | This paper | https://github.com/crazyhottommy/pyflow-RNAseq |
| IGV | (Robinson et al., 2011) | https://software.broadinstitute.org/software/igv/ |
| ggplot2 | (Wickham, 2006) | https://ggplot2.tidyverse.org/ |