| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal anti-H2AK119ub1 | Cell Signaling Technology | Cat# 8240; RRID:AB_10891618 |
| Rabbit polyclonal anti-H3K27me3 | In house (Rose et al., 2016) | n/a |
| Rabbit polyclonal anti-H3K4me3 | In house (Farcas et al., 2012) | n/a |
| Rabbit polyclonal anti-H2A | Millipore | Cat# 07-146; RRID:AB_11212920 |
| Mouse monoclonal anti-H3 | Cell Signaling Technology | Cat# 3638; RRID:AB_1642229 |
| Mouse monoclonal anti-H4 | Cell Signaling Technology | Cat# 2935; RRID:AB_1147658 |
| Rabbit monoclonal anti-RING1B (ChIP) | Cell Signaling Technology | Cat# 5694; RRID:AB_20705604 |
| Mouse monoclonal anti-RING1B (WB) | Atsuta et al., 2001 | n/a |
| Rabbit monoclonal anti-SUZ12 | Cell Signaling Technology | Cat# 3737; RRID:AB_2196850 |
| Rabbit monoclonal anti-EZH2 | Cell Signaling Technology | Cat# 5246; RRID:AB_10694683 |
| Rabbit monoclonal anti-JARID2 | Cell Signaling Technology | Cat# 13594; RRID:AB_2798269 |
| Rabbit polyclonal anti-PCL2 (M96) | GenWay | Cat# GWB-FA7207; RRID:AB_10511542 |
| Rabbit polyclonal anti-EPOP (C17orf96) | Active motif | Cat# 61753; RRID:AB_2793758 |
| Rabbit monoclonal anti-AEBP2 | Cell Signaling Technology | Cat# 14129; RRID:AB_2798398 |
| Rabbit polyclonal anti-PCGF6 | LifeSpan BioSciences | Cat# LS-C482495 |
| Rabbit polyclonal anti-PCGF2 (Mel-18) | Santa Cruz | Cat# sc-10744; RRID:AB_2267885 |
| Rabbit polyclonal anti-PCGF1 | In house (Blackledge et al., 2014) | n/a |
| Mouse monoclonal anti-PHC1 | Cell Signaling Technology | Cat# 13768; RRID:AB_2716803 |
| Rabbit polyclonal anti-CBX7 (WB) | Millipore | Cat# 07-981; RRID:AB_10807034 |
| Rabbit polyclonal anti-KDM2B | In house (Farcas et al., 2012) | n/a |
| Rabbit polyclonal anti-RYBP (DEDAF) | Millipore | Cat# AB3637; RRID:AB_2285466 |
| Rabbit monoclonal anti-BRG1 | Abcam | Cat# ab110641; RRID:AB_10861578 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Methanol-free Formaldehyde | Thermo Fisher Scientific | Cat# 10751395 |
| DSG | Thermo Fisher Scientific | Cat# 11836794 |
| Micrococcal Nuclease | Thermo Fisher Scientific | Cat# EN0181 |
| Proteinase K | Sigma | Cat# P4850 |
| (Z)-4-Hydroxytamoxifen | Sigma | Cat# H7904 |
| SensiMix SYBR No-ROX Kit | Bioline | Cat# QT650-20 |
| Lipofectamine 3000 | Thermo Fisher Scientific | Cat# L3000015 |
| Indole-3-acetic acid sodium salt | Sigma | Cat# I5148 |
| Fluorobrite DMEM | Thermo Fisher Scientific | Cat# A1896701 |
| UBE1 | Boston Biochem | Cat# E-305 |
| UbcH5c | Enzo Life Sciences | Cat# BML-UW9070 |
| Methylated ubiquitin | Boston Biochem | Cat# U-501 |
| 500 nm Janelia Fluor 549 (JF549) | Grimm et al., 2017 | n/a |
| Hoechst 33258 | Thermo fisher Scientific | Cat# H3569 |
| Critical Commercial Assays | ||
| NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) | NEB | Cat# E7335L |
| NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 2) | NEB | Cat# E7500L |
| NEBNext® Ultra™ DNA Library Prep Kit for Illumina® | NEB | Cat# E7370L |
| NEBNext® Ultr™ II FS DNA Library Prep Kit for Illumina | NEB | Cat# E7805L |
| NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® | NEB | Cat# E7760L |
| NEBNext rRNA Depletion Kit (HumanMouseRat) | NEB | Cat# E6310L |
| High Sensitivity DNA Kit for Bioanalyzer | Agilent | Cat# 5067-4626 |
| RNA Pico 6000 Kit for Bioanalyzer | Agilent | Cat# 5067-1513 |
| TURBO DNA-free™ Kit | Thermo Fisher Scientific | Cat# AM1907 |
| Gibson Assembly Master Mix | NEB | Cat# E2611L |
| NextSeq® 500/550 High Output Kit v2 (150 cycles) | Illumina | Cat# FC-404-2002 |
| NextSeq 500/550 High Output v2 Kit (75 cycles) | Illumina | Cat# FC-404-2005 |
| RNeasy Mini Kit | QIAGEN | Cat# 74106 |
| Quick-DNA Miniprep Kit | Zymo Research | Cat# D3024 |
| KAPA Illumina DNA Standards | Roche | Cat# 7960387001 |
| ChIP DNA Clean and Concentrator | Zymo Research | Cat# D5205 |
| Deposited Data | ||
| GEO: GSE132754 | SuperSeries | GEO |
| GEO: GSE132752 | cChIP-seq | GEO |
| GEO: GSE132753 | cRNA-seq | GEO |
| GEO: GSE132751 | CaptureC | GEO |
| Experimental Models: Cell Lines | ||
| Mouse ESC: PRC1CPM | This study | n/a |
| Mouse ESC: PRC1CKO | This study | n/a |
| Mouse ESC: Pcgf4−/−;Pcgf2fl/fl | Fursova et al., 2019 | n/a |
| Mouse ESC: HaloTag-SUZ12;PRC1CPM | This study | n/a |
| Mouse ESC: RING1B-HaloTag;PRC1CPM | This study | n/a |
| Mouse ESC: Ring1a−/−;AID-RING1B (RING1Bdeg) | Rhodes et al., 2019 | n/a |
| Mouse ESC: Control TIR1-only | Rhodes et al., 2019 | n/a |
| Software and Algorithms | ||
| SAMtools (v1.7) | Li et al., 2009 | http://www.htslib.org/ |
| BEDtools (v2.17.0) | Quinlan, 2014 | http://bedtools.readthedocs.io/en/latest/ |
| Bowtie 2 (v2.3.4) | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Sambamba (v0.6.7) | Tarasov et al., 2015 | http://lomereiter.github.io/sambamba/ |
| STAR (v2.5.4) | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| deepTools (v3.1.1) | Ramírez et al., 2014 | https://deeptools.readthedocs.io/en/develop/ |
| MACS2 (v2.1.1) | Zhang et al., 2008 | https://github.com/taoliu/MACS/tree/master/MACS2 |
| UCSC Genome Browser | Kent et al., 2002 | https://genome.ucsc.edu/ |
| Bioconductor (v3.6) | Huber et al., 2015 | https://www.bioconductor.org/ |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| HOMER | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ |
| HiCUP | Wingett et al., 2015 | https://www.bioinformatics.babraham.ac.uk/projects/hicup/ |
| CHiCAGO | Cairns et al., 2016 | http://regulatorygenomicsgroup.org/chicago/ |
| TANGO | Ollion et al., 2013 | https://biophysique.mnhn.fr/tango/ |
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