KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| 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 |