KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| α-macroH2A1.2 | Millipore | Cat#MABE61, RRID:AB_10807977 |
| α-macroH2A1.1 | Cell Signaling Technologies | Cat#12455, RRID:AB_2797923 |
| α-Lig3 | GeneTex | Cat#GTX103172, RRID:AB_2036773 |
| α-FLAG | Agilent | Cat#200472, RRID:AB_10596649 |
| α-PCNA | Santa Cruz | Cat#sc-56, RRID:AB_628110 |
| α-H2B | Abcam | Cat#ab1790, RRID:AB_302612 |
| α-GAPDH | Santa Cruz | Cat#sc-32233, RRID:AB_627679 |
| α-PARP1 | Cell Signaling Technologies | Cat#9542, RRID:AB_2160739 |
| α-H3 | Cell Signaling Technologies | Cat#9715, RRID:AB_331563 |
| α-centromere | Antibodies incorporated | Cat#15-234-0001, RRID:AB_2687472 |
| α-PAR | T revigen | Cat#4335-MC-100, RRID :AB_2572318 |
| α-H3K27me3 | Abcam | Cat#ab6002, RRID:AB_305237 |
| α-phosphor RPA32 (Ser4 / Ser8) | Bethyl | Cat#A300–245A, RRID:AB_210547 |
| Goat anti-mouse IgG-HRP | Santa Cruz | Cat#sc-2005, RRID:AB_631736 |
| Goat anti-rabbit IgG-HRP | Santa Cruz | Cat#sc-2004, RRID:AB_631746 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Aphidicolin | Sigma | Cat#A0781 |
| EdU (5-ethynyl-2’-deoxyuridine) | ThermoFisher Scientific | Cat#E10187 |
| Alexa Fluor 647-azide | ThermoFisher Scientific | Cat#A10277 |
| Hoechst 33342 | ThermoFisher Scientific | Cat#H3570 |
| RO3306 | Selleckchem | Cat#S7747 |
| Alexa Fluor 488–5-dUTP | ThermoFisher Scientific | Cat#C11397 |
| Anti-FLAG M2 Magnetic beads | Sigma | Cat#M8823 |
| Veliparib (PARPi) | Selleckchem | Cat#S1004 |
| Puromycin | Sigma | Cat#P8833 |
| Collagenase II | ThermoFisher Scientific | Cat#17101015 |
| Phytohaemagglutinin | Sigma | Cat#L1668 |
| PI/RNase staining buffer | BD PharMingen | Cat#550825 |
| cOmplete Mini EDTA-free protease inhibitor | Roche | Cat#11836170001 |
| KaryoMAX Colcemid | ThermoFisher Scientific | Cat#15210–040 |
| mLIF | ThermoFisher Scientific | Cat#PMC9484 |
| Doxycycline | Sigma | Cat#D9891 |
| All-trans retinoic acid | Sigma | Cat#R2625 |
| Critical Commercial Assays | ||
| Click-iT EdU Alexa Fluor 647 Imaging Kit | ThermoFisher Scientific | Cat#C10340 |
| Phosphatase inhibitor cocktail set II | Millipore | Cat#524625 |
| SuperscriptIII | ThermoFisher Scientific | Cat#18080044 |
| TURBO DNase | ThermoFisher Scientific | Cat#AM1907 |
| Lipofectamine 2000 | ThermoFisher Scientific | Cat#11668 |
| CGH Bioprime array kit | ThermoFisher Scientific | Cat#18095011 |
| Histone H3 (phospho S10) assay kit | Abcam | Cat#ab115127 |
| 21-color mouse SKY paint kit | Applied spectral imaging | Cat#FPRPR0030 |
| Deposited Data | ||
| Mass spectrometry analyses, see Table S1 | This study | MassIVE: MSV000085351 |
| Experimental Models: Cell Lines | ||
| BJ | ATCC | Cat#CRL-2522, RRID:CVCL_3653 |
| IMR-90 | Coriell | Cat#I90–15, RRID:CVCL_0347 |
| T-REx-293 Cell Line | Thermo Fisher Scientific | Cat#R78007, RRID:CVCL_U427 |
| FLAG-macroH2A1.1 (in HEK293 T-REx) | This study | N/A |
| FLAG-macroH2A1.2 (in HEK293 T-REx) | This study | N/A |
| MCF-7 | ATCC | Cat#HTB-22, RRID:CVCL_0031 |
| Hs 578T | ATCC | Cat#HTB-126, RRID:CVCL_0332 |
| pEJ5 U2OS (cNHEJ) | Gift from Jeremy Stark | N/A |
| pEJ2 U2OS (alt-EJ) | Gift from Jeremy Stark | N/A |
| C57BL/6 Bruce4 ES cells | Lewandoski et al., 1997 | N/A |
| MS2-Xist female ES cells | Jonkers et al., 2008 | N/A |
| pSM33 male ES cells | Engreitz et al., 2013 | N/A |
| macroH2A1.2 WT and KO MEFs | This study | N/A |
| Tail fibroblasts from WT and KO mice | This study | N/A |
| Experimental Models: Organisms/Strains | ||
| MacroH2A1.2 KO mice | This study | NCI Mouse Repository, Cat#01BQO |
| MacroH2A1 KO mice | Changolkar et al., 2007 | N/A |
| β-actin Cre transgenic mice | Lewandoski et al., 1997 | The Jackson Laboratory, Cat#B6N. FVB-Tmem 163Tg(ACTB-cre)2Mrt/CjDswJ |
| Oligonucleotides | ||
| shRNA targeting sequences, see Table S2 | This study | N/A |
| siRNA targeting sequences, see Table S2 | This study | N/A |
| Primers for gene targeting, see Table S3 | This study | N/A |
| Primers for RT-PCR, see Table S3 | This study | N/A |
| Primers for genotyping, see Table S3 | This study | N/A |
| Recombinant DNA | ||
| EJ2 | Gift from Jeremy Stark | RRID :Addgene_44025 |
| pCBASceI | Gift from Maria Jasin | RRID :Addgene_26477 |
| pcDNA3-EGFP | Gift from Doug Golenbock | RRID:Addgene_13031 |
| pEZ-Frt-lox-DT | Gift from Klaus Rajewsky | RRID:Addgene_11736 |
| Full-length mouse Xist plasmid | Gift from Kathrin Plath | N/A |
| pLKO.1 | Gift from David Root | RRID:Addgene_10878 |
| Software and Algorithms | ||
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| FlowJo | BD Biosciences | https://www.flowjo.com |
| Prism | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| Proteome Discoverer 1.4 | ThermoFisher Scientific | https://www.thermofisher.com/us/en/home.html |
| R | R Core Team | http://www.r-project.org |
| KNIME | Berthold et al., 2008 | https://www.knime.com/ |
| HiFish acquisition software | GenASIs, Applied Spectral Imaging | https://spectral-imaging.com/ |
| HiSKY 7.2 | Genasis, Applied Spectral Imaging | https://spectral-imaging.com/ |
| Spot detection algorithm | Olivo-Marin, 2002 | N/A |
| Other | ||
| CellMinerCDB | NIH | https://discover.nci.nih.gov/cellminercdb/ |