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. Author manuscript; available in PMC: 2020 Oct 14.
Published in final edited form as: Cancer Cell. 2019 Sep 26;36(4):402–417.e13. doi: 10.1016/j.ccell.2019.08.006

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