Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-H3 | Abcam | Cat# ab1791 RRID: AB_302613 |
| Mouse monoclonal anti-H3 | Abcam | Cat# ab10799 RRID: AB_470239 |
| Rabbit polyclonal anti-H3K27ac | Active motif | Cat# 39134 RRID: AB_2722569 |
| Rabbit polyclonal anti-H3K56ac | Millipore | Cat# 07–677-I RRID: AB_390167 |
| Rabbit polyclonal anti-H3K27me3 | Millipore | Cat# 07–449 RRID: AB_310624 |
| Rabbit polyclonal anti-H4K20me3 | Abcam | Cat# ab9053 RRID: AB_306969 |
| Rabbit polyclonal anti-H3K36me2 | Abcam | Cat# ab9049 RRID: AB_1280939 |
| Rabbit polyclonal anti-H3K9me3 | Active Motif | Cat# 39161 RRID: AB_2532132 |
| Rabbit polyclonal anti-γH2AX | Abcam | Cat# ab2893 RRID: AB_303388 |
| Rabbit polyclonal anti-γH2AX | Cell Signaling Technology | Cat# 2577 RRID: AB_2118010 |
| Mouse monoclonal anti-γH2AX | Novus | Cat# NBP1–19255 RRID: AB_1642310 |
| Rabbit polyclonal anti-H2AX | Abcam | Cat# ab11175 RRID: AB_297814 |
| Rabbit polyclonal anti-53BP1 | Novus | Cat# NB100–304 RRID: AB_10003037 |
| Rabbit polyclonal anti-P53p | Cell Signaling Technology | Cat# 9284 RRID: AB_331464 |
| Mouse monoclonal anti-P53 | Cell Signaling Technology | Cat# 2524 RRID: AB_331743 |
| Mouse monoclonal anti-ATMp | Cell Signaling Technology | Cat# 4526 RRID: AB_2062663 |
| Rabbit polyclonal anti-p16 | Santa Cruz Biotechnology | Cat# sc-1207 RRID: AB_632106 |
| Rabbit polyclonal anti-PARP1 | Cell Signaling Technology | Cat# 9542 RRID: AB_2160739 |
| Rat monoclonal anti-CD31 | Abcam | Cat# ab56299 RRID: AB_940884 |
| Rabbit polyclonal anti-Laminin | Sigma-Aldrich | Cat# L9393 RRID: AB_477163 |
| Rabbit polyclonal anti-Iba1 | Wako | Cat# 01919741 RRID: 01919741 |
| Rabbit polyclonal anti-GFAP | Antibodies.com | Cat# A85419 RRID: AB_2752917 |
| Mouse monoclonal anti-Lamin A/C | BD Bioscience | Cat# 612163 RRID: AB_399534 |
| Rabbit polyclonal anti-Lamin B1 | Abcam | Cat# ab16048 RRID: ab16048 |
| Rabbit polyclonal anti-macroH2A1 | Active motif | Cat# 39593 RRID: AB_2793271 |
| Mouse monoclonal anti-GAPDH | Millipore | Cat# MAB374 RRID: AB_2107445 |
| Mouse monoclonal anti-TUJ1 | BioLegend | Cat# 801201 RRID: AB_2313773 |
| Rat monoclonal anti-HA-Peroxidase | Roche | Cat# 12013819001 RRID: AB_390917 |
| Mouse monoclonal anti-Oct3/4 | BD Biosciences | Cat# 611203 RRID: AB_398737 |
| Goat polyclonal anti-Klf4 | R&D systems | Cat# AF3158 RRID: AB_2130245 |
| Alexa Fluor® 488 Goat Anti-Mouse IgG (H+L) | Thermo Fisher Scientific | Cat# A-11029 RRID: AB_138404 |
| Alexa Fluor® 568 Goat Anti-Rabbit IgG (H+L) | Thermo Fisher Scientific | Cat# A-11036 RRID: AB_10563566 |
| Alexa Fluor® 568 Donkey Anti- Mouse IgG (H+L) | Thermo Fisher Scientific | Cat# A10037 RRID: AB_2534013 |
| Alexa Fluor® 488 Donkey Anti- Goat IgG (H+L) | Thermo Fisher Scientific | Cat# A32814 RRID: AB_2762838 |
| Anti-rabbit IgG | Millipore | Cat# 12–370 RRID: AB_145841 |
| Bacterial and virus strains | ||
| AAV-DJ-rtTA | Lu et al., 2020 | N/A |
| AAV-DJ-tTA | Lu et al., 2020 | N/A |
| AAV-DJ-OSK | Lu et al., 2020 | N/A |
| AAV-MYO3-tTA | This paper | N/A |
| AAV-MYO3-OSK | This paper | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| (Z)-4-Hydroxytamoxifen | Sigma-Aldrich | Cat# H7904 |
| Tamoxifen citrate salt | Sigma-Aldrich | Cat# T9262 |
| Triamcinolone acetonide | Sigma-Aldrich | Cat# T6501 |
| Etoposide | CALBIOCHEM | Cat# 341205 |
| Camptothecin | CALBIOCHEM | Cat# 208925 |
| Paraquat | SIGMA | Cat# 36541 |
| Hydrogen peroxide | SIGMA | Cat# 216763 |
| Phleomycin | InvivoGen | Cat# ant-ph-1 |
| dCTP [α−32P] | PerkinElmer | Cat# BLU513H500UC |
| L-[35S]-Methionine | PerkinElmer | Cat# NEG709A500UC |
| Recombinant I-PpoI | Promega | Cat# R7031 |
| Rodent Chow Diet | LabDiet | Cat# 5053 |
| LightCycler 480 SYBR Green I Master | Roche | Cat# 4707516001 |
| Dynabeads® Protein A for Immunoprecipitation | Life Technologies | Cat# 10001D |
| Dynabeads® Protein G for Immunoprecipitation | Life Technologies | Cat# 10003D |
| Dynabeads® M-280 Streptavidin | Life Technologies | Cat# 11205D |
| UltraPure™ Buffer-Saturated Phenol | Thermo Fisher | Cat# 15513039 |
| Phenylalanine, L-[2,3,4,5,6–3H] | PerkinElmer | Cat# NET1122001MC |
| Hematoxylin solution modified acc. to Gill II | Millipore | Cat# 1051750500 |
| Eosin Y-solution 0.5% alcoholic | Millipore | Cat# 1024390500 |
| Fluoroshield mounting medium with DAPI | Sigma-Aldrich | Cat# F6057 |
| bFGF | STEM CELL | Cat# 78003.1 |
| ISX9 | CAYMAN CHEM | Cat# 16165 |
| Forskolin | CAYMAN CHEM | Cat# 11018 |
| CHIR99021 | LC Laboratories | Cat# C-6556 |
| I-BET151 | CAYMAN CHEM | Cat# 11181 |
| Fasudil | Selleckchem | Cat# S1573 |
| SB203580 | Selleckchem | Cat# S1076 |
| Dynabeads® Protein A | Thermo Fisher | Cat# 10001D |
| Dynabeads® Protein G | Thermo Fisher | Cat# 10003D |
| AMPure® XP Beads | BECKMAN COULTER | Cat# A63881 |
| Propidium Iodide | Abcam | Cat# ab14083 |
| Premium Grade Fetal Bovine Serum | Seradigm | Cat# 1500–500 |
| Charcoal stripped FBS | VWR | Cat# 35–072-CV |
| Tet System Approved FBS | TAKARA | Cat# 631106 |
| N-2 Supplement | Thermo Fisher Scientific | Cat# 17502001 |
| B-27™ Supplement | Thermo Fisher Scientific | Cat# 17504044 |
| GlutaMAX™ Supplement | Thermo Fisher Scientific | Cat# 35050061 |
| Neurobasal™ Medium | Thermo Fisher Scientific | Cat# 21103049 |
| 0.1% Gelatin | Millipore | Cat# ES-006-B |
| Formaldehyde | CALBIOCHEM | Cat# 344198 |
| Paraformaldehyde | Electron Microscopy Sciences | Cat# 15710 |
| Adenosine-5’-triphosphate disodium salt hydrate | VWR | Cat# AAJ61125–09 |
| NEBNext® High-Fidelity 2X PCR Master Mix | New England Biolabs | Cat# M0541S |
| TRIzol® Reagent | Thermo Fisher Scientific | Cat# 15596–026 |
| VECTASHIELD® PLUS Antifade Mounting Medium | Vector Laboratories | Cat# H-1900–10 |
| cOmplete™ EDTA-free Protease Inhibitor Cocktail | Roche | Cat# 4693132001 |
| Phosphatase Inhibitor Cocktail 2 | SIGMA | Cat# P5726 |
| Phosphatase Inhibitor Cocktail 3 | SIGMA | Cat# P0044 |
| SuperScript® III Reverse Transcriptase | Thermo Fisher Scientific | Cat# 18080093 |
| Critical commercial assays | ||
| E.Z.N.A.® Tissue DNA Kit | Omega Bio-tek | Cat# D3396 |
| E.Z.N.A.® Total RNA Kit I | Omega Bio-tek | Cat# R6834 |
| iScript cDNA synthesis kit | Bio-rad | Cat# 1708891 |
| NEBNext® ChIP-Seq Library Prep Master Mix | New England Biolabs | Cat# NEB E6240L |
| NEBNext® Multiplex Oligos for Illumina | New England Biolabs | Cat# NEB E7335S |
| RNeasy MinElute Cleanup Kit | QIAGEN | Cat# 74204 |
| NEXTflex™ Rapid RNA Sequencing Kit | Bioo Scientific | Cat# 5138–01 |
| NEXTflex™ RNA-Seq Barcodes – 12 | Bioo Scientific | Cat# 512912 |
| Nextera DNA Library Prep Kit | Illumina | Cat# FC-121–1030 |
| Dovetail™ HiChIP MNase Kit | Dovetail Genomics | Cat# 21007 |
| QuantiFluor® dsDNA System | Promega | Cat# E2670 |
| QuantiFluor® RNA System | Promega | Cat# E3310 |
| Library Quantification Kits | Kapa Biosystems | Cat# KK4854 |
| ChIP DNA clean & concentrator | Zymo | Cat# D5201 |
| Surveyor® Mutation Detection Kits | Transgenomic | Cat# 706025 |
| ChIP DNA Clean & Concentrator™ | Zymo Research | Cat# D5201 |
| Click-iT™ EdU Alexa Fluor™ 488 Flow Cytometry Assay Kit | Thermo Fisher Scientific | Cat# C-10425 |
| Senescence β-Galactosidase Staining | Cell Signaling Technology | Cat# 9860 |
| Deposited data | ||
| Next generation sequencing data (ChIP-seq, ATAC-seq, RNA-seq, WGS and Hi-C data) | BioProject ID: PRJNA554729, PRJNA655981 | N/A |
| Experimental models: Cell lines | ||
| WT mouse embryonic fibroblasts | This paper | N/A |
| I-PpoI mouse embryonic fibroblasts | This paper | N/A |
| Cre mouse embryonic fibroblasts | This paper | N/A |
| ICE mouse embryonic fibroblasts | This paper | N/A |
| Cre mouse adult fibroblasts | This paper | N/A |
| ICE mouse adult fibroblasts | This paper | N/A |
| I-SceI mouse embryonic fibroblasts | This paper | N/A |
| 3 mo. OSK-tg mouse adult fibroblasts | This paper | N/A |
| 15 mo. OSK-tg mouse adult fibroblasts | This paper | N/A |
| Experimental models: Organisms/strains | ||
| C57BL/6 mouse | NIA (USA) | N/A |
| C57BL/6 HA-ERT2-I-PpoI mouse | This paper | N/A |
| C57BL/6 Cre-ERT2 mouse | Ruzankina et al., 2007 | N/A |
| I-SceI mouse | Chiarle et al., 2011 | N/A |
| Oligonucleotides | ||
| PCR primers | This paper | Table S1 |
| Recombinant DNA | ||
| pAAV-CMV-rtTA | Lu et al., 2020 | N/A |
| pAAV-CMV-tTA | Lu et al., 2020 | N/A |
| pAAV-TRE3G-OSK | Lu et al., 2020 | N/A |
| pAAVMYO3 | El Andari et al., 2022 | N/A |
| Software and algorithms | ||
| Cellprofiler | Broad Institute | http://cellprofiler.org |
| Ensembl blat | European Bioinformatics Institute | http://www.ensembl.org/Multi/Tools/Blast?db=core |
| GraphPad Prism | GraphPad Software | https://www.grphpad.com |
| Metacore | GeneGo | https://portal.genego.com |
| Galaxy | Penn State University | https://usegalaxy.org |
| GREAT | Stanford University | http://great.stanford.edu/public/html |
| Enrichr | Mount Sinai | http://amp.pharm.mssm.edu/Enrichr |
| ChIP-enrich | University of Michigan | http://chip-enrich.med.umich.edu/chipMain.jsp |
| Easeq | University of Copenhagen | https://easeq.net |
| Primer-BLAST | NIH | https://www.ncbi.nlm.nih.gov/tools/primer-blast |