KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-dimethyl-Histone H3 (Lys4) Antibody | Millipore | Cat# 07-030, RRID:AB_310342 |
| Monoclonal ANTI-FLAG® M2 antibody produced in mouse | Sigma-Aldrich | Cat# F3165, RRID:AB_259529 |
| Recombinant Anti-Histone H3 (tri methyl K9) antibody | Abcam | Cat# ab176916, RRID:AB_2797591 |
| Anti-trimethyl-Histone H3 (Lys27) Antibody | MIllipore | Cat# 07-449, RRID:AB_310624 |
| SRF (H-300) antibody | Santa Cruz Biotechnology | Cat# sc-13029, RRID:AB_2302440 |
| GKLF (H-180) antibody | Santa Cruz Biotechnology | Cat# sc-20691, RRID:AB_669567 |
| Anti-Tet2 Antibody | Sigma-Aldrich | Cat# ABE364 |
| Anti-acetyl-Histone H3 Antibody | Millipore | Cat# 06-599, RRID:AB_2115283 |
| Rabbit IgG, polyclonal - Isotype Control (ChIP Grade) | Abcam | Cat# ab171870, RRID:AB_2687657 |
| Mouse IgG - Isotype Control | Abcam | Cat# ab37355, RRID:AB_2665484 |
| Histone H3K4me2 antibody (pAb) | Active Motif | 39141, RRID:AB_2614985 |
| ANTI-FLAG® antibody produced in rabbit | Sigma-Aldrich | Cat# F7425, RRID:AB_439687 |
| Anti-HA tag antibody - ChIP Grade | Abcam | Cat# ab9110, RRID:AB_307019 |
| 5-hydroxymethylcytosine (5-hmC) monoclonal antibody (mouse) | Diagenode | C15200200-50 |
| 5-methylcytosine (5-mC) Antibody - clone 33D3 | Diagenode | C15200081-100 |
| Monoclonal Anti-Actin, α-Smooth Muscle | Sigma-Aldrich | Cat# A2547, RRID:AB_476701 |
| Rat Anti-Smooth Muscle Myosin Heavy Chain (sml) Monoclonal Antibody, Unconjugated, Clone KM3669 | Kamiya Biomedical Company | Cat# MC-352, RRID:AB_1241986 |
| Anti-TAGLN/Transgelin antibody | Abcam | Cat# ab14106, RRID:AB_443021 |
| Anti-GAPDH antibody [6C5] - Loading Control | Abcam | Cat# ab8245, RRID:AB_2107448 |
| Anti-GAPDH antibody - Loading Control | Abcam | Cat# ab9485, RRID:AB_307275 |
| Anti-Histone H3 antibody - Nuclear Marker and ChIP Grade | Abcam | Cat# ab1791, RRID:AB_302613 |
| H3K4me1 | Millipore | Cat# 07-436, RRID:AB_310614 |
| Anti-Dimethyl Histone H3 (Lys4) Antibody, clone CMA303 | Sigma Aldrich | Cat# 05-1338, RRID:AB_1977248 |
| Phospho-Akt (Ser473) (D9E) XP® Rabbit mAb | Cell Signaling Technology | Cat# 4060, RRID:AB_2315049 |
| Akt1/2/3 Antibody (H-136) | Santa Cruz Biotechnology | Cat# sc-8312, RRID:AB_671714 |
| IRDye® 800CW Donkey anti-Rabbit IgG Secondary Antibody | LI-COR Biosciences | Cat# 926-32211, RRID:AB_621843 |
| IRDye® 680RD Donkey anti-Mouse IgG Secondary Antibody | LI-COR Biosciences | Cat# 926-68072, RRID:AB_10953628 |
| Anti-GFP antibody | Abcam | Cat# ab6673, RRID:AB_305643 |
| Anti-Ki67 antibody | Abcam | Cat# ab15580, RRID:AB_443209 |
| Cleaved Caspase-3 (Asp175) Antibody | Cell Signaling Technology | Cat# 9661, RRID:AB_2341188 |
| DYKDDDDK Tag (D6W5B) Rabbit mAb | Cell Signaling Technology | Cat# 14793, RRID:AB_2572291 |
| Anti-mCherry antibody | Abcam | Cat# ab167453, RRID:AB_2571870 |
| Donkey anti-Goat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 | Molecular Probes | Cat# A-21447, RRID:AB_141844 |
| Donkey Anti-Rat IgG H&L (Alexa Fluor® 555) | Abcam | Cat# ab150154, RRID:AB_2813834 |
| Monoclonal Anti-Actin, α-Smooth Muscle - FITC antibody produced in mouse | Sigma-Aldrich | Cat# F3777, RRID:AB_476977 |
| Anti-Actin, α-Smooth Muscle - Cy3™ antibody, Mouse monoclonal | Sigma-Aldrich | Cat# C6198, RRID:AB_476856 |
| Anti-Tet2 antibody | Abcam | Cat# ab124297, RRID:AB_2722695 |
| Anti-Biotin antibody | Abcam | Cat# ab53494, RRID:AB_867860 |
| Bacterial and Virus Strains | ||
| Ad-m-MYOCD-GFP | Vector Biolabs | Cat# ADV-265349 |
| Ad-mTET2-HA | Applied Biological Materials | Cat# 465200540200 |
| Lenti-Myocd-LSD1 | This paper | N/A |
| Lenti-Myocd-LSD1NF | This paper | N/A |
| Biological Samples | ||
| Human Coronary Artery Smooth Muscle Cells | LONZA | Cat# CC-2583 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Corning® Fetal Bovine Serum, 500 mL, Premium, United States Origin | Corning | Cat# 35-015-CV |
| L-Glutamine (200 mM) | Gibco | Cat# 25030081 |
| L-Ascorbic acid | Sigma-Aldrich | Cat# A4403; CAS: 50-81-7 |
| apo-Transferrin human | Sigma-Aldrich | Cat# T5391; CAS: 11096-37-0 |
| Sodium selenite | Sigma-Aldrich | Cat# S5261; CAS: 10102-18-8 |
| PDGF-BB human | Sigma-Aldrich | Cat# SRP3138 |
| Rapamycin from Streptomyces hygroscopicus | Sigma-Aldrich | Cat# R0395; CAS: 53123-88-9 |
| Retinoic acid | Sigma-Aldrich | Cat# R2625; CAS: 302-79-4 |
| Lipofectamine™ 3000 Transfection Reagent | Invitrogen | Cat# L3000015 |
| Polybrene Infection / Transfection Reagent | Sigma-Aldrich | Cat# TR-1003-G |
| Recombinant Human EGF (Animal-Free) | Biolegend | Cat# 713008 |
| Recombinant Human FGF-basic (146 aa) (Animal-Free) | Biolegend | Cat# 713304 |
| Dynabeads™ Protein G for Immunoprecipitation | Invitrogen | Cat# 10004D |
| ACCUTASE™ Cell detachment solution | Stem cell technologies | Cat# 07922 |
| PowerUp™ SYBR™ Green Master Mix | Applied Biosystems | Cat# A25742 |
| mirVana® miRNA mimic miR-145-5p | ThermoFisher | Cat# MC11480 |
| mirVana® miRNA mimic negative control | ThermoFisher | Cat# 4464058 |
| Lipofectamine RNAiMax Reagent | ThermoFisher | Cat# 13778075 |
| Invitrogen™ CellLight™ Talin-GFP, BacMam 2.0 | Invitrogen | Cat# C10611 |
| Invitrogen™ Alexa Fluor™ 647 Phalloidin | Invitrogen | Cat# A22287 |
| PureCol® Type I Collagen Solution, 3 mg/ml (Bovine) | Advanced BioMatrix | Cat# 5005 |
| Duolink® In Situ PLA Probe anti-rabbit PLUS | Sigma-Aldrich | Cat# DUO92002 |
| Duolink® In Situ PLA Probe anti-mouse MINUS | Sigma-Aldrich | Cat# DUO92004 |
| Duolink® In Situ Detection reagents Orange | Sigma-Aldrich | Cat# DUO92007 |
| Duolink® In Situ mounting medium with DAPI | Sigma-Aldrich | Cat# DUO82040 |
| Histone H3K4me1 Peptide - biotinylated | Active Motif | Cat# 81040 |
| Histone H3K4me2 Peptide - biotinylated | Active Motif | Cat# 81041 |
| Histone H3K4me3 Peptide - biotinylated | Active Motif | Cat# 81042 |
| IRDye 800CW Streptavidin | LI-COR Biosciences | Cat# 926-32230 |
| Methyl-β-cyclodextrin (Cholesterol) | Sigma-Aldrich | Cat# C4555; CAS: 128446-36-6 |
| AdipoRed™ Assay Reagent | LONZA | Cat# PT-7009 |
| Tamoxifen | Sigma-Aldrich | Cat# T5648; CAS: 10540-29-1 |
| Pluronic® F-127 | Sigma-Aldrich | Cat# P2443; CAS: 9003-11-6 |
| 16% Paraformaldehyde Aqueous Solution, EM Grade, Ampoule 10 ML | Electron Microscopy Sciences | Cat# 15710 |
| Crystal violet solution | Sigma-Aldrich | Cat # V5265; CAS: 548-62-9 |
| Antigen Unmasking Solution, Citrate-Based | Vector Laboratories | Cat# H-3300 |
| Critical Commercial Assays | ||
| Qubit™ RNA BR Assay Kit | Invitrogen | Cat# Q10210 |
| iScript™ cDNA Synthesis Kit | Bio-Rad | Cat# 1708891 |
| RNeasy FFPE Kit | Qiagen | Cat# 73504 |
| miRNeasy Mini Kit | Qiagen | Cat# 217004 |
| TaqMan™ MicroRNA Reverse Transcription Kit | Applied Biosystems | Cat# 4366596 |
| Histone Extraction Kit | Abcam | Cat# ab113476 |
| NE-PER Nuclear and Cytoplasmic Extraction Reagents | Thermo Scientific | Cat# 78833 |
| Oil Red O staining kit | Sigma-Aldrich | Cat# MAK194 |
| Rat Mesenchymal Stem Cell Functional Identification Kit | R&D Systems | Cat# SC020 |
| CellTiter-Glo® Luminescent Cell Viability Assay | Promega | Cat# 7570 |
| CUT&Tag-IT™ Assay Kit | Active Motif | Cat# 53160 |
| MeDIP kit | Diagenode | Cat# C02010010 |
| hMeDIP kit | Diagenode | Cat# C02010031 |
| Luciferase assay kit | Promega | Cat# E1500 |
| Deposited Data | ||
| H3K4me3 (Homo Sapiens smooth muscle cell originated from H9) | ENCODE project (Davis et al., 2018) | https://www.encodeproject.org/experiments/ENCSR515PKY/ |
| VSMC_SRF | NCBI's Gene Expression Omnibus | GSM3069844 |
| H3K4me1 (Homo Sapiens smooth muscle cell originated from H9) | ENCODE project (Davis et al., 2018) | https://www.encodeproject.org/experiments/ENCSR130IMV/ |
| H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis | NCBI's Gene Expression Omnibus | GSE179220 |
| H3K4me2 (Homo Sapiens smooth muscle cell originated from H9) | ENCODE project (Davis et al., 2018) | https://www.encodeproject.org/experiments/ENCSR783AXV/ |
| Experimental Models: Cell Lines | ||
| Human coronary artery smooth muscle cells (hCASMCs) | LONZA | Cat# CC-2583 |
| Experimental Models: Organisms/Strains | ||
| Mouse: YFP: B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J | (Srinivas et al., 2001) | MGI: J:80963 |
| Mouse: Myh11-CreERT2: B6.FVB-Tg(Myh11-cre/ERT2)1Soff/J | (Wirth et al., 2008a) | MGI: J:141641 |
| Oligonucleotides | ||
| See Supplementary Table 1 | ||
| Recombinant DNA | ||
| pLVX-Myocd-LSD1-IRES-mCherry | This paper | N/A |
| pLVX-Myocd-LSD1NF-IRES-mCherry | This paper | N/A |
| pGL3-Acta2-CArGWT | (Hendrix et al., 2005) | N/A |
| pGL3-Acta2-promoCArGMut | (Hendrix et al., 2005) | N/A |
| pGL3-Acta2-promo+intCArGMut | (Hendrix et al., 2005) | N/A |
| Software and Algorithms | ||
| Prism 9 | Graph Pad | https://www.graphpad.com/ |
| Adobe Illustrator 2021 | Adobe | https://www.adobe.com/products/illustrator.html |
| Fiji | http://fiji.sc | RRID:SCR_002285 |
| Office 365 | Microsoft | https://www.microsoft.com/en-us/microsoft-365 |
| Adobe Photoshop 2021 | Adobe | https://www.adobe.com/products/photoshop.html |
| R version 4.0.4 | http://www.r-project.org/ | RRID:SCR_001905 |
| Galaxy | http://galaxyproject.org/ | RRID:SCR_006281 |
| Bowtie2 | (Langmead and Salzberg, 2012) | RRID:SCR_016368 |
| Deeptools | (Ramirez et al., 2016) | RRID:SCR_016366 |
| Integrative Genomics Viewer | http://www.broadinstitute.org/igv/ | RRID:SCR_011793 |
| MACS | https://github.com/macs3-project/MACS | RRID:SCR_013291 |
| Diffind | http://bioconductor.org/packages/release/bioc/html/DiffBind.html | RRID:SCR_012918 |
| ChIPseeker | https://bioconductor.org/packages/ChIPseeker/ | RRID:SCR_021322 |
| ClusterProfiler | http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html | RRID:SCR_016884 |
| QIAGEN CLC Genomics Workbench | Qiagen | https://www.qiagen.com/us/products/discovery-and-translational-research/next-generation-sequencing/informatics-and-data/analysis-and-visualization/clc-genomics-workbench/ |
| BaseSpace Correlation Engine | Illumina | https://www.illumina.com/products/by-type/informatics-products/basespace-correlation-engine.html |
| Targetscan | http://targetscan.org/ | RRID:SCR_010845 |
| Ocular Advanced Scientific Camera Control software | Digital Opitcs Limited | https://www.photometrics.com/products/ocular |
| Image Pro Premier | Media Cybernetics | https://www.mediacy.com/support/imagepropremier |
| Other | ||
| Multi Wire Myograph System | DMT | Cat# 620M |
| LEICA Dmi8 Inverted Fluorescent Microscope | LEICA | https://www.leica-microsystems.com/products/light-microscopes/p/leica-dmi8-id/ |
| Nikon Instruments A1 Confocal Laser Microscope | Nikon | https://www.microscope.healthcare.nikon.com/products/confocal-microscopes/a1hd25-a1rhd25 |
| Synergy-HTX multi-mode reader | BioTek | https://www.biotek.com/products/detection-multi-mode-microplate-readers/synergy-htx-multi-mode-reader/ |
| 6.5 mm Transwell® with 8.0 μm Pore Polycarbonate Membrane Insert, Sterile | Corning | Cat# 3422 |
| Bioruptor® Pico sonication device | Diagenode | Cat# B01060010 |
| CFX Connect Realtime System | Bio-Rad | Cat# 1855201 |
| Odyssey® CLx Imaging System | LI-COR Biosciences | https://www.licor.com/bio/odyssey-dlx/ |