KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CHAF1B | Sigma-Aldrich | HPA021679 |
| CHAF1A | Abcam | ab126625 |
| EGR1 | Abcam | ab133695 |
| Sp1 pS739 | Abcam | ab195733 |
| Sp1 | Active Motif | 39058 |
| HA | Santa Cruz | sc-7392 |
| V5 | Sigma-Aldrich | V8012 |
| SRC pY416 | Cell Signaling | 6943S |
| SRC | Cell Signaling | 2109S |
| HP1α | Abcam | ab109028 |
| HP1β | Abcam | ab10478 |
| HP1γ | Abcam | ab10480 |
| RPA1 | Abcam | ab79398 |
| DAXX | Cell Signaling | 4533S |
| HIRA | Abcam | ab129169 |
| ERK1/2 | Cell Signaling | 9102L |
| ERK1/2 pT202/pY204 | Sigma-Aldrich | M9692 |
| E-cadherin | BD Biosciences | 610181 |
| ZO1 | Cell Signaling | 5406S |
| p48 | Abcam | ab79416 |
| Fibronectin | BD Biosciences | 610077 |
| RAS | Cell Signaling | 3339S |
| Actin | Santa Cruz | sc-1615 |
| Vinculin | Sigma-Aldrich | V9264 |
| Histone H3 pS10 | Cell Signaling | 12201S |
| Histone H3 | Active Motif | 61475 |
| Histone H3.1/H3.2 | Millipore | ABE154 |
| Histone H3.3 | Millipore | 09–838 |
| Histone H4 | Abcam | ab10158 |
| Histone H2A | Abcam | ab18255 |
| Histone macro H2A.1 | Abcam | ab37264 |
| anti-Rabit HRP secondary | GE Healthcare | NA934 |
| anti-Mouse HRP secondary | GE Healthcare | NA931 |
| anti-Goat HRP secondary | Millipore | AP180P |
| Histone H3.1/H3.2 (for ChIP-seq) | Active Motif | 61629 |
| Histone H3.3 (for ChIP-seq) | Millipore | 17–10245 |
| RNA Pol II pS5 | Abcam | ab5131 |
| Rabbit IgG | Santa Cruz | sc-2027 |
| CD44 | BD Biosciences | 559942 |
| CD24 | BD Biosciences | 555427 |
| APC mouse IgG2b | BD Biosciences | 555745 |
| FITC mouse IgG2a | BD Biosciences | 553456 |
| Discovery anti-Rabbit HQ | Ventana | 760–4815 |
| Anti-V5 Magnetic beads | MBL International | M215–11 |
| Anti-HA Magnetic beads | Pierce Thermo Scientific | 88836 |
| Biological Samples | ||
| Breast cancer and matched metastatic carcinoma tissue array | Biomax | BR10010e |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Recombinant Human EGF | Peprotech | AF-100–15 |
| Cholera toxin | Sigma-Aldrich | C8052 |
| Insulin | Sigma-Aldrich | I9278 |
| Hydrocortizone | Sigma-Aldrich | H4001 |
| Recombinant Human TGFβ | Peprotech | 100–21 |
| Recombinant Human TNFα | Peprotech | 300–01A |
| Tymidine | Hydrocortizone | Sigma-Aldrich |
| Mithramycin A | Enzo Life Sciences | BML-GR305–0001 |
| KX2–391 | Selleckchem | S2700 |
| Polybrene | Sigma-Aldrich | H9268 |
| Puromycin | Sigma-Aldrich | P7255 |
| G418 Disulfate | Caisson Labs | G030 |
| Blasticidin S HCl | Thermo Fisher | A11139–03 |
| Doxycycline | Millipore | 324385 |
| Carboplatin | Sigma-Aldrich | C2538 |
| Paclitaxel | Sigma-Aldrich | T7191 |
| 16% Paraformaldehyde | Electron Microscopy Sciences | 15710 |
| Crystal Violet | Sigma-Aldrich | C3886 |
| Trypsin | Promega | V511C |
| Lysyl Endopeptidase | Wako | 129–02541 |
| Formalin-D2 | CDN isotopes | D-5933 |
| Formaldehyde solution | Sigma-Aldrich | 252549 |
| Sodium cyanoborohydride | Sigma-Aldrich | 296945 |
| Sodium cyanoborodeuteride | Cambridge Isotope Laboratories Inc | DLM-7364–1 |
| Micrococcal nuclease | Thermo Fisher | 88216 |
| Complete EDTA-free protease inhibitor cocktail | Roche | 5056489001 |
| PhosSTOP phosphatase inhibitor cocktail | Roche | 04906837001 |
| Rat Tail Collagen I | Corning | 354236 |
| BSA | P212121 | CI-00535 |
| Hematoxylin II | Ventana (Roche) | 790–2208 |
| Critical Commercial Assays | ||
| SimplyBlue SafeStain | Invitrogen | LC6065 |
| MycoAlert mycoplasma detection kit | Lonza | LT07–318 |
| X-tremeGENE HP DNA Transfection Reagent | Roche | 06366546001 |
| DC protein Assay kit II | Biorad | 5000112 |
| TBS-based Odyssey blocking buffer | Licor | 927–50150 |
| Amersham ECL detection kit | GE Healthcare | RPN2134 |
| ChromaFlash Chromatin Extraction kit | Epigentek | P-2001–100 |
| PureLink RNA mini kit | Life Technologies | 12183018A |
| QuikChange II XL site directed mutagenesis kit | Agilent Technologies | 200521 |
| iScript cDNA synthesis kit | Bio-Rad | 170–8891BUN |
| SYBR green master mix | Life Technologies | 4312704 |
| TruSeq RNA Sample Prep Kit v2 | Illumina | 15026495 |
| Kapa Library Quantification Kit | Roche | KK4824 |
| LightSwitch Dual Assay kit | Active Motif | 32035 |
| Nextera Library Prep Kit | Illumina | FC-141–1007 |
| MinElute PCR purification kit | Qiagen | 28006 |
| SYBR Green Supermix | Biorad | 1725120 |
| ChIP-IT Express Kit | Active Motif | 53008 |
| ChIP-IT Express Enzymatic Shearing Kit | Active Motif | 53035 |
| Chromatin IP DNA purification kit | Active Motif | 58002 |
| Discovery Amp HQ kit | Ventana (Roche) | 760–052 |
| Discovery ChromoMap DAB kit | Ventana (Roche) | 760–159 |
| LR Clonase II Enzyme Mix | Life Technologies | 11791–100 |
| BP Clonase II Enzyme Mix | Life Technologies | 11789–100 |
| Amplification grade DNase I kit | Sigma-Aldrich | AMPD1–1KT |
| Deposited Data | ||
| ATAC-seq raw data | This paper | GEO: GSE132046 |
| ChIP-seq raw data | This paper | GEO: GSE120313 |
| RNA-seq raw data | This paper | GEO: GSE119030 |
| Mass Spectrometry raw data | This paper | ftp://massive.ucsd.edu/MSV000084205/ |
| Experimental Models: Cell Lines | ||
| MDA-MB-231 parental | (Minn et al., 2005) | parental |
| MDA-MB-231 LM2 | (Minn et al., 2005) | 4175 |
| HEK293T | GenHunter | Q401 |
| MCF-10A | ATCC | CRL-10317 |
| NMuMG | ATCC | CRL-1636 |
| HCC1806 | ATCC | CRL-2335 |
| HCC38 | ATCC | CRL-2314 |
| HCC1937 | ATCC | CRL-2336 |
| SKBR3 | ATCC | HTB-30 |
| HCC116 | ATCC | CCL-247 |
| A549 | ATCC | CCL-185 |
| Experimental Models: Organisms/Strains | ||
| Female nu/nu athymic mice (Hsd:Athymic Nude-Foxn1nu) | Envigo | 069 |
| Oligonucleotides | ||
| Primers Used for Mutagenesis | This paper | See Table S5 |
| Primers Used for Gene Expression qPCR Analysis | This paper | See Table S6 |
| Primers Used for ChIP-qPCR Analysis | This paper | See Table S7 |
| biotinylated DNA fragment of the CHAF1B promoter containing the overlapping Sp1 and EGR1 binding sites (Biotin-5’- TGGCGTCTATGAGTGGGCGGGGCTTC-CCTGGGGTAC) | This paper | N/A |
| biotinylated DNA fragment of the CHAF1B promoter without Sp1 and/or EGR1 consensus binding sequences (Biotin-5’- AAAAATCCTAGAGCAGTTGGCTCC-TCAGATAACCCT) | This paper | N/A |
| Recombinant DNA | ||
| pENTR1A | Addgene | 17398 |
| pCW57.1 | Addgene | 41393 |
| pInducer20 | Addgene | 44012 |
| pLenti Blast | Addgene | 17451 |
| pLKO.1-blast | Addgene | 26655 |
| pLv105-empty | GeneCopoeia | EX-NEG-Lv105 |
| pLvRFP-puro | Vector Builder | This paper |
| pLvGFP-blast | Vector Builder | This paper |
| gagpol | Addgene | 14887 |
| Vsvg | Addgene | 8454 |
| pRSV-Rev | Addgene | 12253 |
| pMDLg/pRRE | Addgene | 12251 |
| pMD2.G | Addgene | 12259 |
| psPax2 | Addgene | 12260 |
| shPASCHA construct | kind gift from Dr. Lukas Dow, WCM | (Dow et al., 2012) |
| pDONR223 | kind gift from Dr. David Sinclair, HMS | (Yoon et al., 2014) |
| pENTRY-GFP | Addgene | 15301 |
| pLenti Blast GFP | This paper | N/A |
| pInducer20 GFP | This paper | N/A |
| pCW57.1 GFP | This paper | N/A |
| pOTB7 CHAF1B | PlasmID HMS | HsCD00330561 |
| pLv105-CHAF1B | GeneCopoeia | EX-T0093-Lv105 |
| pDONR223-CHAF1B | This paper | N/A |
| pCW57.1-CHAF1B | This paper | N/A |
| pENTR1A-CHAF1B T192A/T95C/C198T/A201G/C204A/C207T | This paper | N/A |
| pCW57.1-CHAF1B T192A/T95C/C198T/A201G/C204A/C207T | This paper | N/A |
| pENTR223-EGR1 | PlasmID HMS | HsCD00376208 |
| pCW57.1-EGR1 | This paper | N/A |
| pENTR223-DAXX | PlasmID HMS | HsCD00365258 |
| pCW57.1-DAXX | This paper | N/A |
| pCMV Sport6 HIRA closed | PlasmID HMS | HsCD00337796 |
| pDONR223-HIRA | This paper | N/A |
| pLenti Blast HIRA | This paper | N/A |
| pCW57.1-HIRA | This paper | N/A |
| pDONR221-H3F3A | PlasmID HMS | HsCD00044667 |
| pCW57.1-H3F3A | This paper | N/A |
| pLvH3F3A-V5-blast | Vector Builder | This paper |
| pLvH3F3B-HA-puro | Vector Builder | This paper |
| pENTR1A-H-RAS G12V | Addgene | 22252 |
| pInducer20-H-RAS G12V | This paper | N/A |
| pBABE empty | (Shin et al., 2010) | N/A |
| pBABE-HA-ERK2-D319N | (Shin et al., 2010) | N/A |
| pENTR1A-HA-ERK2-D319N | This paper | N/A |
| pInducer20-HA-ERK2-D319N | This paper | N/A |
| pCMV3-HA-Sp1 | Sino Biologicals | HG12024-NY |
| pENTR1A-HA-Sp1 | This paper | N/A |
| pENTR1A-HA-Sp1 T453A/T739A | This paper | N/A |
| pENTR1A-HA-Sp1 T453E/T739E | This paper | N/A |
| pCW57.1-HA-Sp1 | This paper | N/A |
| pCW57.1-HA-Sp1 T453A/T739A | This paper | N/A |
| pCW57.1-HA-Sp1 T453E/T739E | This paper | N/A |
| empty promoter construct | SwitchGear | S790005 |
| CHAF1B promoter construct | SwitchGear | S718588 |
| CHAF1A promoter construct | SwitchGear | S719853 |
| Cypridine TK control vector | Active Motif | 32036 |
| pLKO.1-Blast shScramble | Addgene | 26701 |
| pLKO.1-puro empty | Kind gift from Dr. Joan Massagué | (Er et al., 2018) |
| pLKO.1-puro shGFP | Sigma-Aldrich | TRCN0000072181 |
| pLKO.1-puro shCHAF1A #1 | Sigma-Aldrich | TRCN0000074273 |
| pLKO.1-puro shCHAF1A #2 | Sigma-Aldrich | TRCN0000234600 |
| pLKO.1-puro shCHAF1B #1 | Sigma-Aldrich | TRCN0000074279 |
| pLKO.1-Blast shCHAF1B #1 | This paper | N/A |
| pLKO.1-puro shCHAF1B #2 | Sigma-Aldrich | TRCN0000074278 |
| pLKO.1-puro shDAXX #1 | Sigma-Aldrich | TRCN0000279732 |
| pLKO.1-puro shDAXX #2 | Sigma-Aldrich | TRCN0000279733 |
| pLKO.1-puro shSp1 #1 | Sigma-Aldrich | TRCN0000285151 |
| pLKO.1-puro shSp1 #2 | Sigma-Aldrich | TRCN0000274208 |
| pLKO.1-puro shHIRA #1 | Open Biosytems | TRCN0000020514 |
| pLKO.1-puro shHIRA #2 | Open Biosytems | TRCN0000020515 |
| dox-inducible mirE-based shH3F3A #1 | RNAi Core facility at MSKCC (Dow et al., 2012) | This paper |
| dox-inducible mirE-based shH3F3A #2 | RNAi Core facility at MSKCC (Dow et al., 2012) | This paper |
| dox-inducible mirE-based shH3F3B #1 | RNAi Core facility at MSKCC (Dow et al., 2012) | This paper |
| dox-inducible mirE-based shH3F3B #2 | RNAi Core facility at MSKCC (Dow et al., 2012) | This paper |
| dox-inducible mirE-based shH3F3A #5 | RNAi Core facility at MSKCC (Dow et al., 2012) | This paper |
| dox-inducible mirE-based shLuciferase | RNAi Core facility at MSKCC (Dow et al., 2012) | This paper |
| Software and Algorithms | ||
| DESeq2 | (Love et al., 2014) | N/A |
| GSEA | (Mootha et al., 2003; Subramanian et al., 2005) | N/A |
| GOseq | (Young et al., 2010) | N/A |
| BWA | (Li and Durbin, 2009) | N/A |
| MACS 2.1.0 | (Zhang et al., 2008) | N/A |
| IGB | (Freese et al., 2016) | N/A |
| SICER | (Li and Durbin, 2009) | N/A |
| SEQUEST v28 revision 13 | (Eng et al., 1994) | N/A |
| Perseus | (Tyanova et al., 2016) | N/A |
| R | The R Foundation | N/A |
| FlowJo v10 | FlowJo LLC | N/A |
| Fiji/Image J | (Rueden et al., 2017; Schindelin et al., 2012) | N/A |
| Visiopharm Image Analysis Apps | Visiopharm | N/A |
| Living Image Software | Perkin-Elmer | N/A |
| Excel 2013 | Microsoft | N/A |
| Prism8 | GraphPad | N/A |
| QuantStudio Real-Time PCR Software v1.3 | Thermo Fisher | N/A |
| Other | ||
| Streptavidin-agarose beads | Sigma-Aldrich | S1638 |
| Nitrocellulose Membrane | GE Healthcare | 10600001/2 |
| Agencourt AMPure SPRI beads | Beckman Coulter | A63882 |
| Protein A magnetic beads (Dynabeads) | Invitrogen | 10002D |
| Protein G magnetic beads (Dynabeads) | Invitrogen | 10004D |
| Cellstripper Non-enzymatic dissociation solution | Corning | 25–056-CI |
| Growth Factor Reduced BioCoat invasion chambers | Corning | 354483 |
| Boyden Chamber inserts | Corning | 353097 |
| Fetal Bovine Serum | Sigma-Aldrich | 12303C |
| Horse Serum | Life Technologies | 16050–122 |
| PicoLab Rodent Diet | Labdiet Purina | 5053 |