| Reagent/resource | Reference/source | Identifier |
|---|---|---|
| Experimental models | ||
| HEK‐293 cells (H. sapiens) | ATCC |
Cat# CRL‐1821; RRID: CVCL_Y481 |
| E14Tg2a.IV (M. musculus) | ATCC |
Cat# CRL‐11268; RRID: CVCL_1926 |
| Recombinant DNA | ||
| FUGW‐GFP‐PML | This paper | NA |
| FUGW‐GFP‐PML‐TurboID | This paper | NA |
| FUGW‐TuboID‐GFP‐PML | This paper | NA |
| FUGW‐GFP‐TRIM33 | This paper | NA |
| FUGW‐GFP‐EV | This paper | NA |
| FUGW‐mCherry‐PML | This paper | NA |
| FUGW‐mCherry‐EV | This paper | NA |
| pCI‐FLAG‐PML | This paper | NA |
| pCI‐FLAG‐TRIM33 | This paper | NA |
| pCI‐FLAG‐TRIM33‐RBCC | This paper | NA |
| pCI‐FLAG‐TRIM33‐PB | This paper | NA |
| pCI‐HA‐PML | This paper | NA |
| pCI‐HA‐PML‐RBCC | This paper | NA |
| pCI‐FLAG‐EV | This paper | NA |
| pCI‐HA‐EV | This paper | NA |
| Antibodies | ||
| Rabbit polyclonal anti TRIM33 Antibody | Bethyl |
Cat# A301‐060A‐1; RRID: AB_2920524 |
| Mouse monoclonal anti‐PML | Merck |
Cat# 36.1‐104; RRID: AB_309932 |
| Mouse monoclonal anti FLAG® M2 antibody | Sigma‐Aldrich |
Cat# F3165; RRID: AB_259529 |
| Rabbit monoclonal anti HA | Millipore |
Cat# 04‐902; RRID: AB_1977526 |
| Mouse monoclonal anti‐GAPDH | ZSGB‐BIO |
Cat# ta‐08; RRID: AB_2747414 |
| Rabbit monoclonal anti‐H3K27ac | Cell Signaling Technology |
Cat# 8173s; RRID: AB_10949503 |
| Rabbit monoclonal anti SMAD2/3 | Cell Signaling Technology |
Cat# D7G7; RRID: AB_2799861 |
| Chemicals, peptides, and recombinant proteins | ||
| Puromycin | Sigma‐Aldrich | Cat# P8833 |
| Polybrene | Sigma‐Aldrich | Cat# TR‐1003 |
| BSA | Amresco | Cat# 332 |
| 2‐Mecraptoethanol | Sigma‐Aldrich | Cat# M3148 |
| Activin A | R&D Systems | Cat# 338‐AC‐010 |
| SB431542 | selleck | Cat# S1067 |
| DMEM | Thermofisher | Cat# C11995500BT |
| L‐Glutamine Solution | Biological Industries | Cat# 02‐020‐1B |
| NEAA | Thermofisher | Cat# 11140050 |
| sodium pyruvate | Sigma‐Aldrich | Cat# S8636 |
| Pen‐Strep‐Ampho.B Solution | Biological Industries | Cat# 03‐033‐1B |
| FBS | ExCell Bio | Cat# FND500 |
| Lipofectamine 2000 | Thermofisher | Cat# 11668019 |
| Opti‐MEM | Thermofisher | Cat# 31985070 |
| Gelatin from porcine skin | Sigma‐Aldrich | Cat# V900863 |
| Lenti‐concentin | Genestar | Cat# C103‐05 |
| Protease Inhibitor Cocktail | Biotool | Cat# B14002 |
| GFP‐Trap Agarose | Chromotek | Cat# gta‐20 |
| Anti‐Flag Affinity Gel | Biotool | Cat# B23102 |
| Protein G Agarose Resin | Smart‐Lifesciences | Cat# 36405ES08 |
| Trypsin–EDTA (0.25%), phenol red | Thermofisher | Cat# 25200072 |
| Critical commercial assays | ||
| FISH Tag DNA Red Kit with Alexa Fluor 594 dye | Thermofisher | Cat# F32949 |
| 2xRealStar Green Mixture qPCR | Genestar | Cat# A311‐TZ10 |
| Total RNA Purification Kit | DAKEWE | Cat# 8034111 |
| RevertAid First Strand cDNA Synthesis Kit | Thermofisher | Cat# K1622 |
| ClonExpress MultiS One Step Cloning Kit | Vazyme | Cat# C113‐02 |
| Deposited data | ||
| RNA‐seq data and ChIP‐seq data | This paper | GEO: GSE199738 |
| Hi‐C data in mESCs | Yan et al (2018) | GEO: GSE74055 |
| TurboID‐PML mass spectrometry | This paper | PRIDE: PXD037432 |
| Lefty1/2 RNA‐seq in D0, D2, D3 and D4 | Wang et al (2017) | GEO: GSE70486 |
| H3K4me3 and H3K27me3 ChIP‐seq in mESCs | Cossec et al (2018) | GEO: GSE99009 |
| SMAD4 ChIP‐seq in mESCs | Wang et al (2019) | GEO: GSE125116 |
| OCT4 and NANOG ChIP‐seq in mESCs | Narita et al (2021) | GEO: GSE146328 |
| H3K18ac and H3K9me3 ChIP‐seq in mESCs | Zuo et al (2022) | GEO: GSE169450 |
| Primers (Oligonucleotides) | ||
| Primers for gRNA and shRNA | This paper Table EV1 | NA |
| Primers for qPCR | This paper Table EV2 | NA |
| Software and Algorithms | ||
| Image J | N/A | https://imagej.nih.gov/ij/; RRID: SCR_003070 |
| GraphPad Prism | GraphPad software (V 8.4.2 (679)) |
https://www.graphpad.com/scientific-%20software/prism/; RRID: SCR_002798 |
| NIS‐Elements | Nikon | https://www.nikoninNikonstruments.com/Products/Software |
| Integrated Genomics Viewer | Thorvaldsdottir et al (2013) | http://software.broadinstitute.org/software/igv/ |
| R | R Core Team (2018) | https://www.r-project.org/ |
| TrimGalore | N/A | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| Bowtie2 v2.1.0 | Langmead & Salzberg (2012) | http://bowtie-bio.sourceforge.net/bowtie2/ |
| PICARD tools | Li et al (2019b) | https://broadinstitute.github.io/picard/ |
| HOMER v3.12 | http://homer.ucsd.edu/homer/motif/ | |
| DeepTools | Ramirez et al (2016) | https://deeptools.readthedocs.io/en/develop/ |
| MACS2 v2.1.1 | Zhang et al (2008) | https://github.com/taoliu/MACS/wiki |
| DiffBind | N/A | https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
| Samtools v0.1.19 | Li et al (2019b) | https://github.com/samtools/samtools |
| FASTQC v0.11.2 | N/A | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| BEDtools v2.17.0 | Quinlan and Hall (2010) | http://bedtools.readthedocs.io/en/latest/ |
| DESeq2 | Love et al (2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Integrative Genomic Viewer | Thorvaldsdottir et al (2013) | http://software.broadinstitute.org/software/igv/ |
| pheatmap | https://cran.r-project.org/web/packages/pheatmap/index.html | |
| Rank ordering of super‐enhancers (ROSE) | https://bitbucket.org/young_computation/rose | |
| Hisat2 v2.1.0 | Pertea et al (2016) | https://daehwankimlab.github.io/hisat2/ |
| cuffdiff v2.2.1 | Trapnell et al (2012) | http://cufflinks.cbcb.umd.edu/ |
| Seurat v3.2.0 | Butler et al (2018) | https://satijalab.org/seurat/ |
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