KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal beta-actin (clone C4) | Santa Cruz | Cat# sc-47778; RRID: AB_626632 |
| Rabbit polyclonal NELF-E (clone H-140) | Santa Cruz | Cat# sc-32912; RRID: AB_2177858 |
| Mouse monoclonal KAP1 (clone 20C1) | Abcam | Cat# ab22553; RRID: AB_447151 |
| Rabbit polyclonal RNA polymerase II (clone N-20) | Santa Cruz | Cat# sc-899; RRID: AB_632359 |
| Rabbit polyclonal CDK9 (clone C-20) | Santa Cruz | Cat# sc-484; RRID: AB_2275986 |
| Rabbit polyclonal NF-κB p65 (clone C-20) | Santa Cruz | Cat# sc-372; RRID: AB_632037 |
| Mouse monoclonal CXCR4, PE conjugated | BD Biosciences | Cat# 555974; RRID: AB_396267 |
| Mouse monoclonal CD4, APC conjugated | Thermo Fisher | S3.5, MHCD0405; RRID: AB_10373698 |
| Mouse monoclonal p24, FITC conjugated | Beckman Coulter | Cat# 6604665; RRID: N/A |
| Rabbit polyclonal anti-human IL-4 | PeproTech | Cat# 500-P24; RRID: AB_1479023 |
| Goat polyclonal anti-human IL-12 | PeproTech | Cat# 500-P154; RRID: AB_148144 |
| Mouse IgG | Santa Cruz | Cat# sc-2025; RRID: AB_737182 |
| Donkey anti-rabbit IgG, HRP conjugated | Santa Cruz | Cat# sc-2313; RRID: AB_641181 |
| Goat anti-mouse IgG, HRP conjugated | Santa Cruz | Cat# sc-2005; RRID: AB_631736 |
| Deposited Data | ||
| Western blot original scans | This paper | http://doi:10.17632/kvtryf67vg.1 |
| Bacterial and Virus Strains | ||
| Escherichia coli DH5α | Thermo Fisher | Cat# 18265017 |
| Escherichia coli STBL3 | Thermo Fisher | Cat# C737303 |
| HIV-1 NL4–3 | NIH AIDS Reagent Program | Cat# 114 |
| HIV-1 NL4–3-deltaEnv-nLuc-2ANef | Martins et al., 2016 | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Puromycin dihydrochloride | Millipore Sigma | Cat# P8833 |
| Triptolide | Santa Cruz | Cat# sc-200122 |
| Flavopiridol | Millipore Sigma | Cat# F3055 |
| Bryostatin | Millipore Sigma | Cat# B7431 |
| Random decamers | Thermo Fisher | Cat# AM5722G |
| Fast SYBR green master mix | Thermo Fisher | Cat# 4385616 |
| Polyjet | SignaGen | Cat# SL100688 |
| Dynabeads human T activator CD3/CD28 | Thermo Fisher | Cat# 11161D |
| Vorinostat (SAHA) | ApexBio | Cat# MK0683 |
| Human TNF-α | Millipore Sigma | Cat# T6674 |
| PMA | Millipore Sigma | Cat# P8139 |
| DMSO | ACROS Organics | Cat# 610420010 |
| Human TGF-β1 | PeproTech | Cat# 100–21 |
| Human IL-2 | NIH AIDS Reagent Program | Cat# 126 |
| Nelfinavir | NIH AIDS Reagent Program | Cat# 4621 |
| RPMI 1640 | HyClone | Cat# SH30027.FS |
| DMEM | HyClone | Cat# SH30022.FS |
| Fetal Bovine Serum | Millipore Sigma | Cat# F4135 |
| Penicillin-Streptomycin | MP Biomedicals | 091670049 |
| Polybrene | Millipore Sigma | Cat# H9268 |
| PBS | HyClone | Cat# SH30028.02 |
| Paraformaldehyde | Millipore Sigma | Cat# P6148 |
| Cytofix/Cytoperm | Becton Dickinson | Cat# 554714 |
| Dual-Luciferase Reporter Assay System | Promega | Cat# E1960 |
| Nano-Glo Luciferase Assay System | Promega | Cat# N1110 |
| Pierce BCA Protein Assay Kit | Thermo Fisher | Cat# 233225 |
| 10XTris/Glycine/SDS Running Buffer | Bio-Rad | Cat# 1610732 |
| 0.45 μM Nitrocellulose Membrane | Bio-Rad | Cat# 1620115 |
| Tween-20 | Fisher Chemical | Cat# BP337–500 |
| Non-fat Dry Milk | LabScientific | Cat# M0841 |
| Clarity Western ECL Substrate | Bio-Rad | Cat# 1705061 |
| 5” × 7” Blue X-Ray Film | Phenix Research Products | Cat# F-BX57 |
| 8” × 10” Blue X-Ray Film | Phenix Research Products | Cat# F-BX810 |
| Dynabeads CD4 Positive Isolation Kit | Thermo Fisher | Cat# 11331D |
| Neon Transfection System 10 ml Kit | Thermo Fisher | Cat# MPK1096 |
| Neon Transfection System | Thermo Fisher | Cat# MPK5000 |
| Methanol-free formaldehyde | Thermo Fisher | Cat# 28908 |
| PMSF | Millipore Sigma | Cat# P7626 |
| cOmplete, Mini EDTA-free Protease Inhibitor Cocktail | Millipore Sigma | Cat# 04693159001 |
| NP-40 | Thermo Fisher | Cat# 28324 |
| Proteinase K | Thermo Fisher | Cat# 03115828001 |
| RNase A, DNase and Protease-free | Thermo Fisher | Cat# EN0531 |
| Alt-R Cas9 Nuclease V3 | IDT | Cat# 1081058 |
| Critical Commercial Assays | ||
| Dynabeads Protein G | Thermo Fisher | Cat# 10004D |
| M-MuLV Reverse Transcriptase | New England Biolabs | Cat# M0253 |
| Mycoplasma Detection Kit | SouthernBiotech | Cat# 13100–01 |
| Fixable Viability Dye eFluor 450 | Thermo Fisher | Cat# 65-0863-14 |
| Quick-RNA Miniprep Kit | Zymo | Cat# R1055 |
| EasySep Human Naive CD4+ T Cell Isolation kit | Stemcell | Cat# 19555 |
| MinElute PCR Purification Kit | QIAGEN | Cat# 28004 |
| Deposited Data | ||
| Western blot original scans | This paper | Uploaded |
| Experimental Models: Cell Lines | ||
| Jurkat, Clone E6–1 | ATCC | Cat# TIB-152 |
| SUP-T1 | ATCC | Cat# CRL-1942 |
| HEK293FT | Thermo Fisher | Cat# 70007 |
| HEK293T/17 | ATCC | Cat# CRL-11268 |
| U2 OS | ATCC | Cat# HTB-96 |
| J-Lat 6.3 | Jordan et al., 2003 | NIH AIDS Reagent Program Cat# 9846 |
| J-Lat 8.4 | Jordan et al., 2003 | NIH AIDS Reagent Program Cat# 9847 |
| J-Lat 9.2 | Jordan et al., 2003 | NIH AIDS Reagent Program Cat# 9848 |
| J-Lat 10.6 | Jordan et al., 2003 | NIH AIDS Reagent Program Cat# 9849 |
| Jurkat, E4 Clone | Pearson et al., 2008 | N/A |
| Jurkat, 2B2D Clone | Pearson et al., 2008 | N/A |
| Engineered Cell Lines, see Table S1 | This paper | N/A |
| Oligonucleotides | ||
| Primers for RNAi, see Table S2 | Millipore Sigma | N/A |
| Primers for RT-qPCR and ChIP, see Table S3 | Millipore Sigma | N/A |
| TracrRNA | IDT | Cat# 1072532 |
| Scrambled guide RNA | IDT | Cat# 1072544 |
| CXCR4 guide RNA | IDT | N/A |
| NF-κB p65 guide RNA | IDT | N/A |
| KAP1 guide RNA | IDT | N/A |
| Recombinant DNA | ||
| pcDNA4/TO (empty vector) | Thermo Fisher | Cat# V102020 |
| pcDNA3.1+ (empty vector) | Thermo Fisher | Cat# V79020 |
| pBluescript II KS+ | Agilent | Cat# X52327 |
| psPAX2 | Unpublished | Addgene Cat# 12260 |
| pMD2.G | Unpublished | Addgene Cat# 12259 |
| pCMV-VSV-G | Stewart et al., 2003 | Addgene Cat# 8454 |
| pTRIP-LUC | Schoggins et al., 2011 | N/A |
| pLVTHM mCherry | Jadlowsky et al., 2014 | N/A |
| pLKO.1 shRNA control plasmid DNA | Millipore Sigma | Cat# SHC002 |
| pLKO.1-IPTG-3xLacO shRNA control plasmid DNA | Millipore Sigma | Cat#SHC332V |
| DNA Clones Generated in This Study | This paper | See Table S5 |
| Software and Algorithms | ||
| JSim v2.15 (developed by the NSR Physiome Project) | Butterworth et al., 2013) https://www.physiome.org/jsim/ | RRID:SCR_007379 |
| Chemical Master Equation | Hahl and Kremling, 2016 | N/A |
| StochSS 1.9 (using Docker) | (Drawert et al., 2016) http://stochss.org/ | N/A |
| Docker | https://www.docker.com/ | RRID: SCR_016445 |
| FlowJo | TreeStar Inc. | RRID: SCR_008520 |
| FACSDiva | Becton Dickinson | RRID: SCR_001456 |
| Prism (version 7) | GraphPad | RRID: SCR_002798 |
| ImageJ | Schneider et al., 2012 | RRID: SCR:003070 |