KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Mo/Rt Ki67 | Invitrogen | 14–5698-82; RRID:AB_10854564 |
| Rabbit IgG, polyclonal-Isotype Control(ChIP Grade) | Abcam | ab171870; RRID:AB_2687657 |
| Normal Rabbit IgG | Cell Signaling Technology | 2729s; RRID:AB_1031062 |
| pAb Histone H3K27me3 | Active Motif | 39155; RRID:AB_2561020 |
| Tri-Methyl-Histone H3K27 (C36B11) Rabbit | Cell Signaling Technology | 9733S; RRID:AB_2616029 |
| Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 | Invitrogen | A-11008; RRID:AB_143165 |
| Goat anti-rabbit IgG (H+L) HRP conjugated | Bio-Rad | 170–6515; RRID:AB_11125142 |
| Goat anti-mouse IgG (H+L) HRP conjugated | Bio-Rad | 172–1011; RRID:AB_11125936 |
| EZH1 antibody | Active Motif | 61583; RRID:AB_2793687 |
| EZH2 antibody | Cell Signaling Technology | 5246S; RRID:AB_10694683 |
| KDM6A antibody | Cell Signaling Technology | 33510S; RRID:AB_2721244 |
| KDM6B antibody | Active Motif | 61387; RRID:AB_2793615 |
| Guinea Pig anti-Rabbit IgG (Heavy & Light Chain) Antibody - Preadsorbed | antibodies-onlines.com | ABIN101961; RRID:AB_10775589 |
| Anti-Histone H3 (tri methyl K9) antibody - ChIP Grade | Abcam | ab8898; RRID:AB_306848 |
| Histone H3K36me3 antibody (pAb) | Active Motif | 61902; RRID: AB_2615073 |
| Ubiquityl-Histone H2A (Lys119) (D27C4) XP® Rabbit mAb | Cell Signaling Technology | 8240; RRID: AB_10891618 |
| Rpb1 NTD (D8L4Y) Rabbit mAb | Cell Signaling Technology | 14958; RRID: AB_2687876 |
| Rb pAb to Histone H3 | Abcam | ab1791; RRID:AB_302613 |
| Human HNF-4 alpha/NR2A1 MAb | R&D systems | PP-H1415–0C; |
| F4/80 antibody | Cl:A3–1 | BIO-RAD | MCA497GA; RRID:AB_323806 |
| Anti-CD31 antibody | Abcam | ab124432; RRID: AB_2802125 |
| Keratin 17/19 (D4G2) XP® Rabbit mAb | Cell Signaling Technology |
12434; RRID: AB_2797912 |
| Bacterial and Virus Strains | ||
| Biological Samples | ||
| Human liver | Saint Agnes Healthcare, Department of Surgery | Supp. Table 1 |
| Mouse liver, kidney | NIA Rodent Colony | Supp. Table 1 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| 16% Formaldehyde (w/v), Methanol-free | Thermo Fisher Scientific | 28908 |
| Q5 Hot Start High-Fidelity 2X Master Mix | New England Biolabs | M0494S |
| MNase (in salt fraction studies) | New England Biolabs | M0247S |
| MNase (in AFM studies) | Sigma | N3755–500UN |
| SPRI beads | Beckman coulter | B23318 |
| TriPure Isolation Reagent | Sigma Aldrich | 11667157001 |
| 2.5% normal goat serum | Vector Biolabs | S-1012–50 |
| DPX mountant for histology | Sigma Aldrich | 06522 |
| Antigen Unmasking Solution, Citrate-Based | Vector Biolabs | H-3300–250 |
| ProLong Gold Antifade reagent | Invitrogen | P36934 |
| Epredia Lab Vision PermaFluor Aqueous Mounting Medium | Fisher Scientific | TA006FM |
| Critical Commercial Assays | ||
| Zymo-Seq RiboFree Total RNA Library Kit | Zymo Research | R3000 |
| ERCC ExFold RNA Spike-In Mixes | Thermo Fisher Scientific | 4456739 |
| SimpleChIP® Plus Sonication Chromatin IP Kit | Cell Signaling Technology |
56383 |
| Nuclei Isolation Kit | Invent Biotechnologies | NI-024 |
| RNeasy Mini Kit | Qiagen | 74104 |
| QIAshredder | Qiagen | 79656 |
| QIAquick Gel Extraction Kit | Qiagen | 28706 |
| RNase-Free DNase Set | Qiagen | 79254 |
| Dovetail Micro-C Kit | Dovetail Genomics | 21006 |
| NEBNext Ultra II DNA Library Prep Kit for Illumina | New England Biolabs | E7645L |
| NEBNext Library Quant Kit for Illumina | New England Biolabs | E7630L |
| NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) | New England Biolabs | E6440L |
| MagMeDIP Kit | Diagenode | C02010021 |
| High-capacity cDNA to RNA kit | Thermo Fisher Scientific | 4387406 |
| Qubit 1X dsDNA, High Sensitivity Assay Kit | Thermo Fisher Scientific | Q33231 |
| Qubit RNA, High Sensitivity Assay Kit | Thermo Fisher Scientific | Q32852 |
| Qubit RNA, Broad Range Assay Kit | Thermo Fisher Scientific | Q10210 |
| Qubit RNA Integrity and Quality (IQ) Assay Kit | Thermo Fisher Scientific | Q33221 |
| DNA 1000 kit | Agilent | 5067–1504 |
| DNA HS kit | Agilent | 5067–4626 |
| Liquid DAB+, 2-component system, Immunohistochemistry Visualization | Agilent | K346711–2 |
| Deposited Data | ||
| All sequencing data (GEO super series) | This paper | GEO: GSE185708 |
| RNA-seq | This paper | GEO: GSE185705 |
| ChIP-seq | This paper | GEO: GSE185704 |
| Salt fraction DNA-seq | This paper | GEO: GSE185707 |
| CUT&Tag | This paper | GEO: GSE185703 |
| Histone modification ChIP-seq data of mouse heart and quadriceps muscle |
Sleiman et al, 2020 47 | SRA: SRP162386 |
| meDIP | This paper | GEO: GSE223480 |
| Mass spec histone modifications | Chorus | chorusproject.org/1736 |
| Western blot | MendeleyData | doi: 10.17632/7wkwn9vw3f.1 |
| Immunofluorescence (IF) | MendeleyData | doi: 10.17632/7wkwn9vw3f.1 |
| Immunohistochemistry (IHC) | MendeleyData | doi: 10.17632/7wkwn9vw3f.1 |
| Transmission Electron Microscopy (TEM) | MendeleyData | doi: 10.17632/7wkwn9vw3f.1 |
| PhenoImager | MendeleyData | doi: 10.17632/7wkwn9vw3f.1 |
| Atomic Force Microscopy (AFM) | MendeleyData | doi: 10.17632/7wkwn9vw3f.1 |
| Experimental Models: Cell Lines | ||
| HepG2 | ATCC | HB-8065 |
| HeLa | ATCC | CCL-2 |
| Experimental Models: Organisms/Strains | ||
| Mouse (C56BL/6JN) | NIA Rodent Colony | Supp. Table 1 |
| Oligonucleotides | ||
| Primers for Ezh1 | GGTTCCTGCTGTCCTCTATTT | TCCACAGCACCTCACTTTATC |
| Primers for Ezh2 | GCTGATGCCCTGAAGTATGT | GGCAGCTGTTTCAGAGAGAA |
| Primers for Kdm6a | CATTACCATCCGCCTCATCTT | GGTGCAGAACTGGGTTACTT |
| Primers for Kdm6b | GCTAGCTGTGATCCCTGTATATG | AGAGGTGAGTGGGACTGTTA |
| Primers for Dnmt1 | AGGCTGCTACCAAGGACTA | CACAGACACTGAGCACAAGA |
| Primers for Mki67 | CAGGGATCTCAGCGCAATTA | GAGCTTTATTGGATAGGACAGAGG |
| Primers for Suv39h1 | TTGCAGGCCTCTTCATTACTC | GCTTGATGTTAGGCTGGTATCT |
| Recombinant DNA | ||
| Software and Algorithms | ||
| GO | Huang da et al, 200978 | https://david.ncifcrf.gov/summary.jsp; RRID:SCR_001881 |
| GraphPad Prism/9.0.0 (121) | Dotmatics | https://www.graphpad.com/ |
| DRAGEN FASTQ Generation/3.7.4 | Illumina | https://support.illumina.com/downloads/dragen-workflow-fastq-installer.html |
| bowtie/2–2.4.2 | Langmead and Salzberg, 201279 | http://bowtie-bio.sourceforge.net/index.shtml; RRID:SCR_016368 |
| trimgalore/0.6.6 | N/A |
https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/; doi 10.5281/zenodo.5127898 |
| STAR/2.7.5b | Dobin et al, 201364 | https://github.com/alexdobin/STAR; RRID:SCR_004463 |
| samtools/1.10 | Li et al., 200965 | http://www.htslib.org/doc/samtools.html; RRID:SCR_002105 |
| picard/2.20.8 | N/A | https://broadinstitute.github.io/picard/; RRID:SCR_006525 |
| Rsubread/2.6.4 | Liao et al, 201966 |
https://bioconductor.org/packages/release/bioc/html/Rsubread.html; RRID:SCR_009803 |
| DESeq2/1.30.1 | Love et al, 201467 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html; RRID:SCR_015687 |
| ImpulseDE2/0.99.10 | Fischer et al, 201842 | https://bioconductor.riken.jp/packages/3.9/bioc/html/ImpulseDE2.html |
| Gene Set Enrichment Analysis (GSEA/4.1.0) | Subramanian et al, 200580 | https://www.gseamsigdb.org/gsea/msigdb/index.jsp; RRID:SCR_003199 |
| Complex Heatmap/2.6.2 | Gu et al, 201669 | https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html |
| Sambamba/0.7.1 | Tarasov et al, 201572 | https://github.com/biod/sambamba/releases |
| deepTools/3.5.0 | Ramirez et al. 201473 | https://deeptools.readthedocs.io/en/develop/; RRID:SCR_016366 |
| peakranger/1.18 | Feng et al, 201181 | http://ranger.sourceforge.net/; RRID:SCR_010863 |
| DiffBind/3.2.6 | Stark et al, 201174 |
https://bioconductor.org/packages/release/bioc/html/DiffBind.html; RRID:SCR_012918 |
| diffReps/1.55.6 | Shen et al, 201375 | https://github.com/shenlab-sinai/diffreps; RRID:SCR_010873 |
| EDD | Lund et al, 201422 | https://github.com/CollasLab/edd; RRID:SCR_001693 |
| DANPOS | Chen et al, 201328 | https://sites.google.com/site/danposdoc/; RRID:SCR_015527 |
| BEDTools | Quinlan et al, 201082 | https://bedtools.readthedocs.io/en/latest/; RRID:SCR_006646 |
| All code in this paper (Github) | This paper | https://doi.org/10.5281/zenodo.7789081 |
| Other | ||
| DMEM (4.5g/L glucose) | Thermo Fisher Scientific | 11965126 |
| PBS | Thermo Fisher Scientific | 14190136 |
| Trypsin (0.25%) | Thermo Fisher Scientific | 25200056 |
| FBS | Thermo Fisher Scientific | 16000044 |
| Penicillin-Streptomycin Solution, 100X | Thermo Fisher Scientific | 15140122 |