KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-β-actin | Cell Signaling | Cat# 4967 |
| Rabbit anti-CD31 | Abcam | Cat# ab28364 |
| Mouse anti-FLAG M2-Peroxidase (HRP) | Sigma-Aldrich | Cat# A8592 |
| Mouse anti-FLAG M2 | Sigma-Aldrich | Cat# F1804 |
| Rabbit anti-GFP (D5.1) | Cell Signaling | Cat# 2956 |
| Rabbit anti-Hdac3 | Abcam | Cat# ab7030 |
| Mouse anti-Hdac3 (B-12) | Santa Cruz | Cat# sc-17795 |
| Rabbit anti-alpha smooth muscle Actin | Abcam | Cat# ab5694 |
| Mouse anti-H3K9me2 | Abcam | Cat# ab1220 |
| Rabbit anti-H3K9me2 | Active Motif | Cat# 39239 |
| Rabbit anti-H3K9me3 | Abcam | Cat# ab8898 |
| Rabbit anti-H3K27me2 | Active Motif | Cat# 39246 |
| Rabbit anti-H3K27me3 | EMD Millipore | Cat# 07-499 |
| Rabbit anti-phospho-Histone H3 (Ser10) | Cell Signaling | Cat# 9701 |
| Rabbit anti-H4K20me2 | Abcam | Cat# ab9052 |
| Rabbit anti-H4K20me3 | Abcam | Cat# ab9053 |
| Rabbit anti-Lamin B1 | Abcam | Cat# ab16048 |
| Goat anti-Lamin B (M-20) | Santa Cruz | Cat# sc-6217 |
| Mouse anti-Troponin T, cardiac isoform Ab-1 | ThermoFisher | Cat# MS-295-P |
| Mouse anti-Cardiac Troponin T (13–11) | ThermoFisher | Cat# MA5-12960 |
| Mouse anti-SMRT (mouse ascites) | M.A. Lazar lab | N/A |
| normal Rabbit IgG | Cell Signaling | Cat# 2729 |
| normal Mouse IgG | Santa Cruz | Cat# sc-3878 |
| normal Goat IgG | Santa Cruz | Cat# sc-2028 |
| Secondary Antibodies | ||
| Chicken anti-mouse AlexaFluor 488 | Invitrogen | Cat# A21200 |
| Goat anti-rabbit AlexaFluor 647 | Invitrogen | Cat# A21244 |
| Donkey anti-Rabbit AlexaFluor 488 | Invitrogen | Cat# A21206 |
| Donkey anti-Rabbit AlexaFluor 568 | Invitrogen | Cat# A10042 |
| Donkey anti-Rabbit AlexaFluor 647 | Invitrogen | Cat# A31573 |
| Donkey anti-Mouse AlexaFluor 488 | Invitrogen | Cat# A21202 |
| Donkey anti-Mouse AlexaFluor 568 | Invitrogen | Cat# A10037 |
| Donkey anti-Goat AlexaFluor 488 | Invitrogen | Cat# A11055 |
| Donkey anti-Goat AlexaFluor 647 | Invitrogen | Cat# A21447 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Red dUTP | Abbott Laboratories | Cat# 02N34-040 |
| Human H3K9me2 peptide | Abcam | Cat# ab1772 |
| Human H3K9me3 peptide | Abcam | Cat# ab1773 |
| Human H3K27me2 peptide | Abcam | Cat# ab1781 |
| Lamin B1 (B-10) Blocking Peptide | Santa Cruz | Cat# sc-6217P |
| Anti-FLAG magnetic beads | Sigma-Aldrich | Cat# M8823 |
| MEK1 inhibitor PD98059 | Cell Signaling | Cat# 9900 |
| 4-Hydroxytamoxifen | Sigma-Aldrich | Cat# T176 |
| Critical Commercial Assays | ||
| Nick Translation kit | Abbott Laboratories | Cat# 32-801300 |
| Duolink | Sigma-Aldrich | Cat# DUO92101 |
| NEBNext Ultra II DNA Library Kit for Illumina | New England Biolabs | Cat# E7645L |
| NextSeq 500/550 High Output v2 kit (75 cycles) | Illumina | FC-404-2005 |
| GeneChip™ WT Plus Reagent Kit | ThermoFisher | Cat# 902280 |
| GeneChip™ Mouse Gene 2.0 ST Array | ThermoFisher | Cat# 902500 |
| Deposited Data | ||
| All genomics data | This paper | GSE97878 |
| Myocyte signature gene set | This paper | GSE47948 |
| Pluripotent ESC gene expression | This paper | GSE36114 |
| E8.5 endoderm cell gene expression | This paper | GSE40823 |
| Endothelial cell gene expression | This paper | GSE52564 |
| H3K27me3 ChIP-seq dataset | ENCODE | GSM1000089 |
| H3K9me3 ChIP-seq dataset | ENCODE | GSM1000147 |
| Experimental Models: Cell Lines | ||
| Mouse: ESC, CCE | Kyoto University | 129/Sv CCE |
| Mouse: ESC, CMV-creERT; Hdac3f/f | This paper | N/A |
| Mouse: C2C12 | ATCC | Cat# CRL-1772 |
| Human: 293T Lenti-X™ cells | Clontech | Cat# 632180 |
| Experimental Models: Organisms/Strains | ||
| Mus Musculus, Mixed, Islet1Cre/+ | S. Evans lab | Now available: Jackson Labs #024242 |
| Mus Musculus, Mixed, Nkx2-5Cre/+ | R.J. Schwartz lab | Now available: Jackson Labs #030047 |
| Mus Musculus, Mixed Hdac3 flox | M.A. Lazar Lab | Now available: Jackson Labs #024119 |
| Mus Musculus, Mixed CMV-creERT | Jackson Labs | Cat# 004682 |
| Mus Musculus, Mixed NS-DADm | M.A. Lazar lab (You et al., 2013) | N/A |
| Oligonucleotides | ||
| Cre-specific genotyping (5’-TGC CAC GAC CAA GTG ACA GC-3’, 5’-CCA GGT TAC GGA TAT AGT TCA TG-3’) | This paper | N/A |
| floxed Hdac3 allele (5’-GCA GTG GTG GTG AAT GGC TT-3’, 5’-CCT GTG TAA CGG GAG CAG AAC TC-3’) | This paper | N/A |
| qPCR primers, see Table S6 | This paper | N/A |
| qRT-PCR primers, see Table S6 | This paper | N/A |
| shRNA oligonucleotides, see Table S6 | This paper | N/A |
| Recombinant DNA | ||
| BAC Mouse RP23-310F9 | ThermoFisher | Cat# RPCI23.C |
| BAC Mouse RP23-196J13 | ThermoFisher | Cat# RPCI23.C |
| BAC Mouse RP23-80E16 | ThermoFisher | Cat# RPCI23.C |
| BAC Mouse RP23-187H18 | ThermoFisher | Cat# RPCI23.C |
| BAC Mouse RP23-207G7 | ThermoFisher | Cat# RPCI23.C |
| BAC Mouse RP23-150M6 | ThermoFisher | Cat# RPCI23.C |
| pEGFP-Lap2β | Euroscarf.de | Cat# P30463 |
| pCMX-SMRT | M.A. Lazar lab | N/A |
| pcDNA3 -Hdac3-FLAG | P. Gallinari lab | N/A |
| pcDNA3 -Hdac3-Y298H–FLAG | P. Gallinari lab | N/A |
| pFUGW-Hdac3-FLAG | This paper | N/A |
| pFUGW-Hdac3-Y298H–FLAG | This paper | N/A |
| pFUGW-Hdac3-FLAG- Lap2β | This paper | N/A |
| pFUGW-Hdac3-Y298H–FLAG- Lap2β | This paper | N/A |
| pFUGW-Δ33-70 Hdac3-FLAG | This paper | N/A |
| psPAX2 | Addgene | Cat# 12260 |
| pMD2.G | Addgene | Cat# 12259 |
| FUGW-GFP | Addgene | Cat# 14883 |
| Software and Algorithms | ||
| IMARIS 8 | Bitplane | http://www.bitplane.com/releasenotes/imaris800.aspx |
| Huygenes Professional | Scientific Volume Imaging | https://svi.nl/HuygensProfessional |
| GraphPad Prism 7 | GraphPad Software, Inc. | https://www.graphpad.com |
| Affymetrix Command Console and Expression Console | ThermoFisher | https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/affymetrix-genechip-command-console-software.html |
| Partek Genomics Suite v6.6 | Partek | http://www.partek.com/pgs |
| Significance Analysis of Microarrays v2.0 | Open Source | https://github.com/MikeJSeo/SAM |
| STAR aligner | Open Source | https://github.com/alexdobin/STAR |
| Picard tools | Open Source | http://broadinstitute.github.io/picard/ |
| Bamtools v2.4.1 | Open Source | https://github.com/pezmaster31/bamtools |
| DeepTools2 | Open Source | https://github.com/fidelram/deepTools |
| Enriched Domain Detector | (Lund et al., 2014) | https://github.com/CollasLab/edd |
| Bedtools suite v2.26 | Open Source | https://github.com/arq5x/bedtools2/releases |