| Antibodies |
|
|
|
| H3K27me3 |
Cell Signaling |
Cat#9733; RRID: AB_2616029 |
| H2AK119ub |
Cell Signaling |
Cat#8240; RRID: AB_10891618 |
| RING1B |
Cell Signaling |
Cat#5694; RRID: AB_10705604 |
| CBX7 |
Abcam |
Cat#ab21873; RRID: AB_726005 |
| DEDAF (RYBP) |
Millipore |
Cat#AB3637; RRID: AB_11213333 |
| JHDM1B (KDM2B) |
Millipore |
Cat#09–864; RRID: AB_10806072 |
| EZH2 |
Cell Signaling |
Cat#5246; RRID: AB_10694683 |
| MTF2 |
Proteintech |
Cat#16208–1-AP; RRID: AB_2147370 |
| JARID2 |
Cell Signaling |
Cat#13594; RRID: AB_2798269 |
|
| Chemicals, peptides, and recombinant proteins |
|
| Heparin Sodium Salt |
Sigma-Aldrich |
Cat#H3149 |
| FGF4 Recombinant Human Protein |
Gibco |
Cat#PHG0154 |
| RPMI 1640 |
Gibco |
Cat#11875093 |
| DMEM, high glucose, sodium pyruvate |
Gibco |
Cat#11995073 |
| Fetal Bovine Serum, qualified |
Gibco |
Cat#26140079 |
| Penicillin-Streptomycin |
Gibco |
Cat#15140122 |
| L-glutamine |
Gibco |
Cat#25030081 |
| MEM Non-essential Amino Acids |
Gibco |
Cat#11140050 |
| Sodium Pyruvate |
Gibco |
Cat#11360070 |
| β-mercaptoethanol |
Sigma-Aldrich |
Cat#63689 |
| LIF |
Lif-1Cα/COS-conditioned ESC media |
N/A |
| Trypsin-EDTA, phenol red |
Gibco |
Cat#2520072 |
| LipoFectamine 3000 |
Invitrogen |
Cat#L3000015 |
| 10X Phosphate-Buffered Saline (PBS) |
Corning |
Cat#46–013-CM |
| Pierce 16% Formaldehyde |
Thermo Scientific |
Cat#28906 |
| 37% Formaldehyde |
Fisher Scientific |
Cat#BP531–500 |
| TRIzol Reagent |
Invitrogen |
Cat#15596026 |
| Chloroform |
Fisher Scientific |
Cat#BP1145–1 |
| 25:24:1 Phenol:Chloroform:Isoamyl Alcohol |
Sigma-Aldrich |
Cat#6805 |
| Protein A/G PLUS Agarose Beads |
Santa Cruz Biotechnology |
Cat#sc-2003 |
| AMPure XP Beads |
Beckman Coulter |
Cat#A63880 |
| Dynabeads M-280 Streptavidin |
Invitrogen |
Cat#11205D |
| Dynabeads MyOne Streptavidin C1 |
Invitrogen |
Cat#65002 |
| Ribonuclease A (RNase A) from bovine pancreas |
Sigma-Aldrich |
Cat#R4642 |
| Proteinase K Solution |
Bioline |
Cat#BIO-37084 |
| Proteinase K (Fungal) |
Invitrogen |
Cat#25530015 |
| Linear Acrylamide |
Invitrogen |
Cat#AM9520 |
| Choice Taq |
Denville |
Cat#CB4050–2 |
| Phusion High-Fidelity DNA Polymerase |
New England Biolabs |
Cat#M0530S |
| Biotin-16-dUTP |
Roche |
Cat#11093070910 |
| Terminal Deoxynucleotidyl Transferase |
Thermo Scientific |
Cat#EP0161 |
| Klenow Fragment (3'->5' exo) |
New England Biolabs |
Cat#M0212S |
|
| dATP Solution |
Invitrogen |
Cat#10–216-018 |
|
| Critical commercial assays |
|
| Neon Transfection System 100μL Kit |
Invitrogen |
Cat#MPK10025 |
| QIAquick Nucleotide Removal Kit |
Qiagen |
Cat#28304 |
| Zymo Research RNA Clean & Concentrator |
Zymo Research Kit |
Cat#50–125-1669 |
| Arima-HiC + Kit |
Arima Genomics |
Cat#A510008 |
| KAPA RNA HyperPrep with RiboErase |
Roche/KAPA Biosystems (HMR) |
Cat#KK8561 |
| NEBNext End Repair Module |
New England Biolabs |
Cat#E6050S |
| Quick Ligation Kit |
New England Biolabs |
Cat#M2200S |
| NEBNext High-Fidelity 2X PCR Master Mix |
New England Biolabs |
Cat#M0541S |
| High-Capacity cDNA Reverse Transcription Kit |
Applied Biosystems |
Cat#4368814 |
| iTaq Universal SYBR Green Supermix |
Bio-Rad |
Cat#1725125 |
| PureLink HiPure Plasmid Midiprep Kit |
Invitrogen |
Cat#K2100004 |
|
| Deposited data |
|
| Raw and analyzed sequencing data |
This study; see Table S4
|
GEO: GSE217262
|
| Mouse reference genome NCBI build 37, NCBI37/mm9 |
Genome Reference Consortium |
https://www.ncbi.nlm.nih.gov/grc/mouse
|
| Variant sequence data |
Sanger Institute |
https://www.sanger.ac.uk/data/mouse-genomes-project/
|
|
| Experimental models: Cell lines |
|
| Mouse: C/B and B/C trophoblast stem cells |
This study |
N/A |
| Mouse: E14 embryonic stem cells |
This study |
N/A |
| Mouse: DR4 embryonic fibroblast cells |
ATCC |
Cat#SCRC-1045 |
|
| Oligonucleotides |
|
| CRISPR-Cas9 sgRNAs, see Table S5
|
This study |
N/A |
| Genotyping PCR primers, see Table S5
|
This study |
N/A |
| qPCR primers, see Table S5
|
This study |
N/A |
|
| Recombinant DNA |
|
| PB_tre_dCas9_VP160 vector |
Schertzer et al.55
|
Cat#126031;https://doi.org/10.1261/rna.068932.118
|
| PB_tre_Cas9 vector |
Schertzer et al.55
|
Cat#126029;https://doi.org/10.1261/rna.068932.118
|
| PB_rtTA_BsmBI vector Schertzer et al.55
|
Schertzer et al.55
|
Cat#126028;https://doi.org/10.1261/rna.068932.118
|
| pUC19-piggyBac transposase |
Schertzer et al.55
|
https://doi.org/10.1261/rna.068932.118
|
|
| Software and algorithms |
|
| Custom Scripts |
This study |
https://github.com/aki-kb/calabrese_lab/tree/main/braceros_airn_2023;https://doi.org/10.5281/zenodo.7988247
|
| Juicer/Juicebox (v1.5.6) |
Durand et al.27,28
|
https://github.com/aidenlab/juicer;https://github.com/aidenlab/Juicebox
|
| Juicer Tools (v1.9.9) |
Durand et al.27
|
https://github.com/aidenlab/juicer
|
| HiCExplorer (v3.7.2) |
Wolff et al.,56 Ramirez et al.57
|
https://hicexplorer.readthedocs.io/en/latest
|
| Bowtie2 (v2.4.5) |
Langmead and Salzberg58
|
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
|
| STAR (v2.7.9a) |
Dobin et al.58
|
https://github.com/alexdobin/STAR
|
|
| Samtools (v1.16) |
Li et al.59 |
https://github.com/samtools/samtools
|
| Bedtools (v2.30) |
Quinlan and Hall60 |
https://bedtools.readthedocs.io/en/latest
|
| Significant Peak Interaction (SIP; v1.5) |
Rowley et al.43
|
https://github.com/PouletAxel/SIP
|
| MACS2 (v2.1.2) |
Zhang et al.61
|
https://github.com/taoliu/MACS
|
| Subread: featureCounts (v1.6.3) |
Liao et al.62
|
http://subread.sourceforge.net
|
| RStudio (v4.2.0) |
N/A |
https://posit.co/products/open-source/rstudio
|
| ggplot2, ggpubr (v3.3.5) |
Wickham63
|
https://ggplot2.tidyverse.org
|
| GraphPad Prism (v9.4.1) |
N/A |
https://www.graphpad.com
|
|
| Other |
|
| Vibra-Cell™ VCX 130 Sonicator & 6mm Probe |
Sonics |
Cat#H-1002–2 |
| Bioruptor® Plus sonication device |
Diagenode |
Cat#B01020001 |
