Antibodies |
anti-HCF-1 rabbit polyclonal Ab#2124 |
Kristie Laboratory |
RRID:AB_2636976 |
anti-HCF-1 rabbit polyclonal Ab#2130 |
Kristie Laboratory |
RRID:AB_2636977 |
anti-MED12 rabbit polyclonal |
Bethyl Laboratories |
Cat# A300-774A; RRID:AB_669756 |
anti-AFF4 rabbit polyclonal |
Bethyl Laboratories |
Cat# A302-538A; RRID:AB_1998985 |
anti-AFF4 rabbit polyclonal |
Bethyl Laboratories |
Cat# A302-539A; RRID:AB_1998983 |
anti-BRD4 rabbit polyclonal |
Bethyl Laboratories |
Cat# A301-985A; RRID:AB_1576498 |
anti-CDK9 rabbit polyclonal |
Santa Cruz Biotech. |
Cat# sc-484; RRID:AB_2275986 |
anti-PAF1 rabbit polyclonal |
Bethyl Laboratories |
Cat# A300-172A; RRID:AB_309394 |
anti-SUPT16H rabbit polyclonal |
Santa Cruz Biotech. |
Cat# sc-28734; RRID:AB_661341 |
anti-SETD1A rabbit polyclonal |
Abiocode |
Cat# R0196-2; RRID:AB_2636972 |
anti-RbBP5 rabbit polyclonal |
Bethyl Laboratories |
Cat# A300-109A; RRID: AB_210551 |
anti-GAPDH mouse monoclonal |
Santa Cruz Biotech. |
Cat# sc-32233; RRID:AB_627679 |
anti-VP16 rabbit polyclonal |
Sigma-Aldrich |
Cat# V4388; RRID:AB_261865 |
anti-ICP4 mouse monoclonal |
Virusys |
Cat# H1A021; RRID:AB_2636973 |
anti-UL29 (ICP8) rabbit polyclonal |
Gift of William Ruyechan, University of Buffalo, SUNY |
RRID:AB_2636974 |
anti-NELFA goat polyclonal |
Santa Cruz Biotech. |
Cat# sc-23599; RRID: AB_2241683 |
anti-RNAPII-o (RNAPII 8WG16) mouse monoclonal |
Covance |
Cat# MMS-126R; RRID: AB_10013665 |
anti-RNAPII-S5p (H14) mouse monoclonal |
Covance |
Cat# MMS-134R; RRID: AB_10063994 |
anti-RNAPII-S2p (H5) mouse monoclonal |
Covance |
Cat# MMS-129R; RRID: AB_10063704 |
anti-RNAPII-S2p rabbit polyclonal |
Abcam |
Cat# Ab5095; RRID: AB_304749 |
anti-POLR2B rabbit polyclonal |
Santa Cruz Biotech. |
Cat# sc-67318; RRID: AB_2167642 |
Normal Rabbit IgG |
Millipore |
Cat# 12-370; RRID: AB_145841 |
anti-Rabbit Alexa 488 |
Jackson ImmunoResearch Labs |
Cat# 711-545-152; RRID: AB_2313584 |
anti-Rabbit Alexa 594 |
Jackson ImmunoResearch Labs |
Cat# 711-585-152; RRID: AB_2340621 |
anti-Mouse Alexa 594 |
Jackson ImmunoResearch Labs |
Cat# 715-585-150; RRID: AB_2340854 |
Bacterial and Virus Strains |
HSV-1 (strain F) |
Gift of B. Roizman, University of Chicago |
|
hCMV (strain RC256) |
ATCC |
VR-2356 |
Chemicals, Peptides, and Recombinant Proteins |
HMBA (N, N’-Hexamethylene bis(acetamide)) |
Sigma-Aldrich |
CAS: 564468-51-5; Cat# 224235 |
JQ1+ |
APExBIO/Cayman Chemical/Biovison |
CAS: 1268524-70-4; Cat# A1910/Cat #11187/Cat# 2070 |
JQ1− |
APExBIO/Cayman Chemical/Biovision |
CAS: 1268524-71-5; Cat# A8181/Cat# 106/Cat# 2384 |
dBET1 |
Chemietek |
CAS: 1799711-21-9; Cat# CT-DBET1 |
I-BET762 |
Cayman Chemical |
CAS: 1260907-17-2; Cat# 10676 |
Flavopiridol |
Santa Cruz Biotech. |
CAS: 146426-40-6; Cat# sc-202157 |
i-CDK9 (N2’-(trans-4-aminocyclohexyl)-5’-chloro-N6-(3-fluorobenzyl)-2,4’-bipyridine-2’,6-diamine) |
MedChem Express |
CAS: 1263369-28-3; Cat# HY-16462 |
Acyclovir |
Sigma-Aldrich |
CAS: 59277-89-3; Cat# A4669 |
Vehicle (DMSO; Dimethyl sulfoxide) |
Sigma-Aldrich |
CAS: 67-68-5; Cat# D2650 |
Critical Commercial Assays |
ISOLATE II RNA Mini Kit |
Bioline |
Cat# BIO-52073 |
Maxima first-strand cDNA synthesis kit |
ThermoFisher Scientific |
Cat# K1671 |
Quanta qScript microRNA cDNA Synthesis Kit |
Quanta Biosciences |
Cat# 95107 |
Dynabeads™ Antibody Coupling Kit |
ThermoFisher Scientific |
Cat# 14311D |
Sequence-Based Reagents |
siGENOME siRNA SMARTpool targeting BRD2 |
GE Dharmacon |
M-004935-02 |
siGENOME siRNA SMARTpool targeting BRD3 |
GE Dharmacon |
M-004936-01 |
siGENOME siRNA SMARTpool targeting AFF1 |
GE Dharmacon |
M-020074-02 |
siGENOME Individual siRNA targeting AFF4: AFF4-1 |
GE Dharmacon |
M-020276-02-0001 |
siGENOME Individual siRNA targeting AFF4: AFF4-2 |
GE Dharmacon |
M-020276-02-0004 |
FlexiTube Individual siRNA targeting BRD4: BRD4-1 |
Qiagen |
SI03190845 |
FlexiTube Individual siRNA targeting BRD4: BRD4-2 |
Qiagen |
SI04307009 |
Non-targeting siControl |
GE Dharmacon |
D-001206-13, D-001206-14 |
Experimental Models: Cell Lines |
MRC5; Normal human lung fibroblast |
ATCC |
CCL-171 |
HFF; Human Foreskin Fibroblast (TERT-immortalized) |
Gift of T. Shenk, Princeton University |
|
HEK-293; Human Embryonic Kidney |
ATCC |
CRL-1573 |
Vero |
ATCC |
CCL-81 |
Experimental Models: Organisms/Strains |
BALB/c mice, Female, 6–8 weeks old |
Taconic |
BALB/cAnNTac |
Oligonucleotides |
Primers used in this study are listed in Table S2
|
|
|
Software and Algorithms |
Imaris (v8.2.0) |
BITPLANE |
|
SEQUEST (v1.2)/Proteome Discoverer (v1.3) |
ThermoFisher |
|
Scaffold (v4.2.1) |
Proteome Software Inc.; http://www.proteomesoftware.com/products/scaffold/
|
|
SAINTexpress |
http://www.crapome.org |
|
ReactomeFIViz/Cytoscape (v3.4.0) |
http://www.cytoscape.org/ |
|
GeneTools image analysis software/G:BOX Chemi XT4 |
Syngene;http://www.syngene.com/
|
|
Other |
TriPure Isolation reagent |
Roche/Sigma-Aldrich |
Cat# 11667157001 |
Lysing Matrix D Tubes |
MP-Biomedicals |
Cat# 6913 |