KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal anti- BRD4 | Bethyl | Cat# A700–004; RRID: AB_2631885 |
| Rabbit polyclonal anti-BRD4 | Santa Cruz biotechnology | Cat# sc-48772; RRID: AB_2065729 |
| Mouse monoclonal anti-BRD4 | Sigma | Cat# AMAB90841; RRID: AB_2665685 |
| Mouse monoclonal anti-BRD3 | Santa Cruz biotechnology | Cat# sc-81202; RRID: AB_1119692 |
| Rabbit monoclonal anti-BRD2 | abcam | Cat# ab139690; RRID: AB_2737409 |
| Mouse monoclonal anti-DYKDDDDK tag | GenScript | Cat# A00187; RRID: AB_1720813 |
| Mouse monoclonal anti- Nucleolin (C23, clone MS-3) | Santa Cruz biotechnology | Cat# sc-8031; RRID: AB_670271 |
| Mouse monoclonal anti-JNK | Santa Cruz biotechnology | Cat# sc-7345; RRID: AB_675864 |
| Mouse monoclonal anti-pJNK | Santa Cruz biotechnology | Cat# sc-6254; RRID: AB_628232 |
| Mouse monoclonal anti-CDK9 | Santa Cruz biotechnology | Cat# sc-13130; RRID: AB_627245 |
| Mouse monoclonal anti-Pol II | Santa Cruz biotechnology | Cat# sc-56767; 8WG16; RRID: AB_627245 |
| Mouse monoclonal anti-Vimentin | Santa Cruz biotechnology | Cat# sc-373717; RRID: AB_10917747 |
| Rabbit polyclonal anti-CDK9 pThr186 | Millipore-sigma | Cat# SAB4504223; N/A |
| Rat monoclonal anti-Pol II-CTD pSer-5 | Millipore | Cat# 04–1572;3E8; RRID: AB_10615822 |
| Rat monoclonal anti-Pol II-CTD pSer-2 | Millipore | Cat# 04–1571;3E10; RRID: AB_11212363 |
| Rat monoclonal anti-Pol II-CTD pSer-7 | Millipore | Cat# 04–1570;4E12; RRID: AB_10618152 |
| Mouse monoclonal anti-FLAG | Sigma | Cat# F3165; RRID: AB_259529 |
| Rabbit polyclonal anti-β-Tubulin | abcam | Cat# ab6046; RRID: AB_2210370 |
| Rabbit monoclonal anti-MYC | abcam | Cat# ab32072; Y69; RRID: AB_731658 |
| Rabbit monoclonal anti-MYC pThr58 | abcam | Cat# ab185655; RRID: AB_2920883 |
| Rabbit polyclonal anti- Histone AcH3K122 | abcam | Cat# ab33309; RRID: AB_942262 |
| Rabbit monoclonal anti-Histone H3 | Cell Signaling | Cat# 4499; RRID: AB_10544537 |
| Rabbit polyclonal anti- Phospho-c-Jun (Ser63) | Cell Signaling | Cat# 9261; RRID: AB_2130162 |
| Rabbit polyclonal anti- PP2AC | Cell Signaling | Cat# 2038; RRID: AB_2169495 |
| Mouse monoclonal anti-E-Cadherin | Cell Signaling | Cat# 14472; 4A2; RRID: AB_2728770 |
| Rabbit polyclonal anti-PP2AC | Cell Signaling | Cat# 2038, RRID: AB_2169495 |
| Rabbit polyclonal anti-PPP4C | Proteintech | Cat# 10262–1-AP, RRID: AB_2300020 |
| Rabbit recombinant anti-BRD4 | Active Motif | Cat# 91301, RRID: AB_2813829 |
| Mouse recombinant anti-RNA Pol II | Active Motif | Cat# 91151, RRID: AB_2793789 |
| Rat monoclonal anti-CD4 | Thermo Fisher Sci | Cat# 47–0042-82, RRID: AB_1272183 |
| Rat monoclonal anti-CD8 | Thermo Fisher Sci | Cat# MCD0828, RRID: AB_10372364 |
| Hamster monoclonal anti-CD69 | Biolegend | Cat# 104508, RRID: AB_313111 |
| Rabbit polyclonal anti-BRD4 pThr1186 | Vivitude; This study | Custom; N/A |
| Rabbit polyclonal anti-BRD4 pThr1212 | Vivitude; This study | Custom; N/A |
| IRDye®680RD Goat anti-mouse IgG Secondary Antibody | LI-COR Biosciences | Cat# P/N: 926–68070; RRID: AB_10956588 |
| IRDye® 800CW Goat anti-Rabbit IgG Secondary Antibody | LI-COR Biosciences | Cat# P/N: 926–32211; RRID: AB_621843 |
| Chemicals, peptides, and recombinant proteins | ||
| Phorbol 12-myristate 13-acetate (PMA) | Sigma | Cat# P1585; N/A |
| Ionomycin | Sigma | Cat# I0634; N/A |
| Anisomycin | GoldBio | Cat# A-580–25; N/A |
| SP600125 JNK inhibitor | Selleckchem | Cat# S1460; N/A |
| D-JNK-1 JNK inhibitor | MedChemExpress | Cat# HY-P0069; N/A |
| Nodularin inhibitor | Enzo Life Sciences | Cat# ALX-350–061-C100; N/A |
| Cisplatin | Enzo Life Sciences | Cat# ALX-400–040-M250; N/A |
| Lipopolysaccharide (LPS) | Thermo Fisher Sci | Cat# 00–4976-03; N/A |
| (+)-JQ1 inhibitor | BPS Bioscience | Cat# 27401; N/A |
| Ni-NTA Agarose beads | Qiagen | Cat# 30210; N/A |
| Anti-DYKDDDDK G1 Affinity Resin | GenScript | Cat# L00432; N/A |
| Protein A/G Magnetic Beads | Thermo Scientific | Cat# 88803; N/A |
| Benzonase | Sigma | Cat# E1014; N/A |
| RNase-Free DNase Set | QIAGEN | Cat# 79254; N/A |
| Anti-FLAG Peptide | Sigma | Cat# F-3290; N/A |
| Custom peptide Ac-CQKQEPKTPVAPK-amide |
Vivitude; This study | N/A |
| Custom peptide Ac-CQKQEPK(pT)PVAPK -amide |
Vivitude; This study | N/A |
| Custom peptide Ac-CVQKHPTTPS-amide |
Vivitude; This study | N/A |
| Custom peptide Ac-CVQKHPT(pT)PS-amide |
Vivitude; This study | N/A |
| Histone H3.3 Human, Recombinant | New England Biolabs | Cat# M2507S; N/A |
| Recombinant Human c-Myc | RayBiotech | Cat# 230–00580-100; N/A |
| Recombinant human GST-JNK1 | SignalChem | Cat# M33–10G-10; N/A |
| Recombinant human GST-JNK2 | SignalChem | Cat# M34–10BG-10; N/A |
| Recombinant human His-JNK1 | Thermo Fisher Sci | Cat# PV3319; N/A |
| Recombinant human Protein Phosphatase 2A C | Cayman chemical | Cat# 10011237; N/A |
| Recombinant human Protein Phosphatase PPP4C | MyBioSource, Inc. | Cat# MBS142407; N/A |
| Critical commercial assays | ||
| SimpleChIP Plus Enzymatic Chromatin IP Kit | Cell Signaling Technology | Cat# 9005; N/A |
| Re-ChIP-IT kit | Active Motif | Cat# 53016; N/A |
| EpiMark Nucleosome Assembly Kit | New England Biolabs | Cat# E5350S; N/A |
| RNAeasy Plus mini kit | Qiagen | Cat# 74134; N/A |
| RNase-Free DNase Set | Qiagen | Cat# 79254; N/A |
| Duolink® In Situ Red Starter Kit Mouse/Rabbit | Sigma | Cat# DUO92101; N/A |
| SuperScript™ III First-Strand Synthesis System | Thermo Scientific | Cat# 18080051; N/A |
| SYBR™ Green PCR Master Mix | Thermo Scientific | Cat# 4309155; N/A |
| RNA 6000 Nano Kit | Agilent | Cat# 5067–1511; N/A |
| Quick-Load® Taq 2X Master Mix | New England BioLabs | Cat# M0271L; N/A |
| Deposited Data | ||
| RNA-seq data | This study | GEO; GSE252982 |
| ChIP-seq data | This study | GEO; GSE252982 |
| Mass spec proteomics data | This study | MassIVE; MSV000093873 |
| All original images | This study | http://dx.doi.org/10.17632/mfz7x3zxg6.1 |
| Experimental Models: Cell Lines | ||
| PC3 Cell Line | ATCC | RRID: CVCL_0035 |
| HCT116 Cell Lines | ATCC | CCL-247; RRID: CVCL_0291 |
| DLD1 cell line | ATCC | RRID: CVCL_0248 |
| DLD1-BRD4-IAA7 cell line | Dr. Ali Shilatifard; 43 | N/A |
| Recombinant DNA | ||
| Mouse WT-BRD4-FLAG in the pFAST Bac1 baculovirus transfer vector | Dr. Dinah Singer; 8 | N/A |
| Murine Flag-His-BRD4 WT (1–1402 amino acids) in the pAcHLT-C baculovirus transfer vector | Dr. Kieko Ozato; 45 | N/A |
| Murine Flag-His-BRD4 ΔN, ΔC, ΔB1, ΔB2 and ΔB1B2 mutants in the pAcHLT-C baculovirus transfer vector | Dr. Keiko Ozato; 45 | N/A |
| Mouse BRD4-FLAG S1153A, T1222A, T1248A, S1153A+T1222A, T1222A+T1248A and the 3A mutants in the pFAST Bac1 baculovirus transfer vector | This study | N/A |
| Human WT-BRD4-FLAG in the pCDNA5 mammalian vector | Dr. Kornelia Polyak; 46 | Addgene plasmid #90331 |
| Human 3A-BRD4-FLAG in the pCDNA5 mammalian vector | This study | N/A |
| BRD4-FLAG F1, F2, F3 and F4 fragments in the pET11 bacterial vector | Dr. Dinah Singer; 26 | N/A |
| Flag-WT JNK1, JNK2, and Flag-JNK1 APF, JNK2 APF dominant negative mutants in the pCDNA3 mammalian vector | Dr. Roger Davis; 47 | Addgene plasmids #13798, #13755, #13846 and #13761 |
| Software and Algorithms | ||
| Image studio Lite | Li-Cor | https://www.licor.com/islite |
| ImageJ | National Institutes of Health; 48 | https://imagej.nih.gov/ij/ |
| NIS-Elements 4.5 | Nikon | https://www.microscope.healthcare.nikon.com/products/software/nis-elements |
| Bowtie2 | GitHub; 49 | https://github.com/BenLangmead/bowtie2 |
| MACS | GitHub; 50 | https://github.com/taoliu/MACS |
| STAR aligner for sequence alignment RNA-seq analysis | GitHub; 51 | https://github.com/alexdobin/STAR |
| rMATS for alternative splicing analysis | SourceForge; 52 | http://rnaseq-mats.sourceforge.net |
| rmats2sashimiplot | GitHub | https://github.com/Xinglab/rmats2sashimiplot |
| String 11.5 | String Consortium | https://string-db.org |
| db SUPER | Tsinghua University | http://asntech.org/dbsuper |
| EnhancerAtlas 2.0 | Enhanceratlas.org | http://enhanceratlas.org/ |
| Proteome Discoverer 2.4 | Thermo Fisher Sci | RRID:SCR_014477 |