Strain, strain background (Escherichia coli) | E.coli DH5α: F-, φ 80dlacZ ΔM15, Δ(lacZYA -argF )U169, deoR , recA1 , endA1 , hsdR17 (rK-, mK+), phoA, supE44 , λ-, thi −1, gyrA96 , relA1 | Takara | Cat#9057 | |
Strain, strain background (Escherichia coli) | E. coli HB101: F-, hsdS20(rB-, mB-), recA13, ara-14, proA2, lacY1, galK2, rpsL20 (str), xyl-5, mtl-1,supE44, leuB6, thi-1. | Takara | Cat#9051 | |
Strain, strain background (Escherichia coli) | E.coli BL21: F-, ompT, hsdSB (rB-mB-), gal, dcm | Takara | Cat#9126 | |
Strain, strain background (Escherichia coli) | E.coli Stbl3: F-, mcrB, mrr, hsdS20 (rB-, mB-), recA13, supE44, ara-14, galK2, lacY1, proA2, rpsL20 (StrR), xyl-5, λ- leu, mtl-1 | ThermoFisher | Cat#C7381201 | |
Cell line (Homo sapiens) | HEK293T | ATCC | CRL-3216; RRID: CVCL_0063 | female |
Cell line (Homo sapiens) | HeLa | ATCC | CCL-2; RRID: CVCL_0030 | female |
Cell line (Homo sapiens) | TZM-bl | NIH AIDS Reagent Program | Cat#8129 | female |
Cell line (Homo sapiens) | J-Lat 6.3 | PMID: 12682019 | NIH AIDS Reagent Program Cat#9846 | Dr. Eric Verdin (The Buck Institute for Research on Aging, Novato, CA, USA) |
Cell line (Homo sapiens) | J-Lat 8.4 | PMID: 12682019 | NIH AIDS Reagent Program Cat#9847 | Dr. Eric Verdin (The Buck Institute for Research on Aging, Novato, CA, USA) |
Cell line (Homo sapiens) | J-Lat 9.2 | PMID: 12682019 | NIH AIDS Reagent Program Cat#9848 | Dr. Eric Verdin (The Buck Institute for Research on Aging, Novato, CA, USA)
|
Cell line (Homo sapiens) | J-Lat 10.6 | PMID: 12682019 | NIH AIDS Reagent Program Cat#9849 | Dr. Eric Verdin (The Buck Institute for Research on Aging, Novato, CA, USA) |
Cell line (Homo sapiens) | J-Lat 15.4 | PMID: 12682019 | NIH AIDS Reagent Program Cat#9850 | Dr. Eric Verdin (The Buck Institute for Research on Aging, Novato, CA, USA) |
Biological sample (Homo sapiens) | Blood samples from healthy individuals | Guangzhou Blood Center, Guangzhou | http://www.gzbc.org/ | |
Biological sample (Homo sapiens) | Blood samples from HIV-1- infected individuals | Department of Infectious Diseases, Guangzhou 8th People’s Hospital, Guangzhou | http://gz8h.com.cn/ | |
Antibody | Mouse Monoclonal anti-TRIM28 Antibody | Proteintech | Cat#66630–1-Ig; RRID: AB_2732886; Lot#10006062 | (1:1000) |
Antibody | Rabbit Polyclonal anti-TRIM28 Antibody | Proteintech | Cat#15202–1-AP; RRID: AB_2209890; Lot#00051172 | (1:1000) |
Antibody | Rabbit Polyclonal Anti-Histone H3 (tri methyl K4) Antibody | Abcam | Cat#ab8580; RRID: AB_306649; Lot#GR273043-3 | Use 2 µg for 25 µg of chromatin |
Antibody | Rabbit Polyclonal Anti-Histone H3 (acetyl K9) Antibody | Abcam | Cat#ab4441; RRID: AB_2118292; Lot#GR270585-1 | Use 2 µg for 25 µg of chromatin |
Antibody | Mouse Monoclonal Anti-Histone H3 (tri methyl K27) Antibody | Abcam | Cat#ab6002; Lot#GR275911-3 | Use 5 µg for 25 µg of chromatin |
Antibody | Normal Rabbit Anti-IgG Antibody | CST | Cat#2729; RRID: AB_1031062 | Use 1 µg for 25 µg of chromatin |
Antibody | Rabbit Polyclonal Anti-UBE2I Antibody | Abclonal | Cat#A2193; Lot#45473 | (1:1000) |
Antibody | Rabbit Polyclonal Anti-UBA2 Antibody | Abclonal | Cat#A4363 | (1:1000) |
Antibody | Rabbit Polyclonal Anti-SAE1 Antibody | Proteintech | Cat#10229–1-AP; RRID: AB_2182917; Lot#00040591 | (1:1000) |
Antibody | Rabbit Monoclonal Anti-SUMO4 Antibody | Abcam | Cat#ab126606; RRID: AB_11128131; Lot#GR851138-12 | (1:1000) |
Antibody | Rabbit Monoclonal Anti-CDK9 (C12F7) Antibody | CST | Cat#2316; Lot#6 | (1:1000) |
Antibody | Rabbit Polyclonal Anti-SENP3 Antibody | Proteintech | Cat#17659–1-AP; RRID: AB_2301618; Lot#00025621 | (1:1000) |
Antibody | Rabbit Polyclonal Anti-RNA polymerase II CTD repeat YSPTSPS (phosphor-Ser2) Antibody | Abcam | Cat#ab5095; RRID: AB_304749; Lot#GR278215-1 | Use 2 µg for 25 µg of chromatin |
Antibody | Mouse Monoclonal Anti-Histone H3 (di methyl K9) Antibody | Abcam | Cat#ab1220; RRID: AB_449854 | Use 4 µg for 25 µg of chromatin |
Antibody | Rabbit Polyclonal Anti-Histone H3 (tri methyl K9) Antibody | Abcam | Cat#ab8898; RRID: AB_306848 | Use 4 µg for 25 µg of chromatin |
Antibody | Donkey Anti-Mouse IgG H and L (Alexa Fluor 647) Antibody | Abcam | Cat#ab150107; Lot#GR311164-3 | (1:200) |
Antibody | Donkey Anti-Rabbit IgG H and L (Alexa Fluor 647) Antibody | Abcam | Cat#ab150075; Lot#GR3174006-4 | (1:200) |
Antibody | Donkey Anti-Rabbit IgG (H + L), Highly Cross- Adsorbed, CF 568 Dye Conjugates, Single Label for STORM | Biotium | Cat#20803–500 μl; Lot#17C0626 | (1:200) |
Antibody | Donkey Anti-Mouse IgG (H + L), Highly Cross- Adsorbed, CF 568 Dye Conjugates, Single Label for STORM | Biotium | Cat#20802–500 μl; Lot#17C1004 | (1:200) |
Antibody | Rabbit Anti-DDDDK Tag Polyclonal Antibody, Unconjugated | MBL | Cat#PM020; RRID: AB_591224; Lot#026 | (1:1000) |
Antibody | Mouse Monoclonal Anti-HA-Tag Antibody | MBL | Cat#M180-3; RRID: AB_10951811; Lot#008 | (1:10000) |
Antibody | Mouse Monoclonal Anti-His-Tag Antibody | Proteintech | Cat#66005–1-Ig; RRID: AB_11232599; Lot#00083246 | (1:1000) |
Antibody | Rabbit Polyclonal Anti-GAPDH Antibody | Proteintech | Cat#10494–1-AP; RRID: AB_2263076; Lot#00039889 | (1:10000) |
Antibody | IRDye 680RD Goat anti-Mouse IgG (H + L), 0.5 mg Antibody | LI-COR Biosciences | Cat#926–68070; RRID: AB_10956588; Lot#C70613-15 | (1:10000) |
Antibody | IRDye 800CW Goat Anti-Rabbit IgG, Conjugated Antibody | LI-COR Biosciences | Cat#926–32211; RRID: AB_621843; Lot#C70620-05 | (1:10000) |
Antibody | PerCP-Cy 5.5 Mouse Anti-Human CD45RO | BD Biosciences | Cat#560607; RRID: AB_1727500; Lot#5338941 | (1:1000) |
Antibody | APC/Cy7 anti- human CD45RA | BioLegend | Cat#304127; RRID: AB_10708419; Lot#B164612 | (1:1000) |
Antibody | Anti-Human CD69 PE-Cy7 | ThermoFisher | Cat#25-0699-42; RRID: AB_1548714; Lot#E10154-1635 | (1:1000) |
Antibody | Anti-Human CD62L PE-Cyanine7 | ThermoFisher | Cat#25-0629-42; RRID: AB_1257142; Lot#4291471 | (1:1000) |
Antibody | Anti-Human CD4 FITC | ThermoFisher | Cat#11-0048-42; RRID: AB_1633390; Lot#E10526-1631 | (1:1000) |
Antibody | PE-Cy5 Conjugated Amti-human CD25 (IL-2R) | ThermoFisher | Cat#15-0259-42; RRID: AB_1944361; Lot#E11289-102 | (1:1000) |
Recombinant DNA reagent | VSV-G glycoprotein- expression vector | PMID: 9306402 | Addgene Plasmid #12259 | Dr. Didier Trono (School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland) |
Recombinant DNA reagent | Lentiviral packaging construct pCMVΔR8.2 | PMID: 9306402 | Addgene Plasmid #12263 | Dr. Didier Trono (School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland) |
Recombinant DNA reagent | Lentiviral construct vector pLKO.3G-RFP | This paper | N/A | Progenitor: pLKO.3G |
Recombinant DNA reagent | Lentiviral construct vector lentiCRISPRv2 | PMID: 25075903 | Addgene Plasmid #52961 | Dr. Feng Zhang (Broad Institute of MIT and Harvard) |
Recombinant DNA reagent | Plasmid: 10His- SUMO1-Q92R | This paper | Supplementary file 3 | Progenitor: pcDNA3.1(+) |
Recombinant DNA reagent | Plasmid: 10His -SUMO2-Q88R | This paper | Supplementary file 3 | Progenitor: pcDNA3.1(+) |
Recombinant DNA reagent | Plasmid: 10His- SUMO4-Q88R | This paper | Supplementary file 3 | Progenitor: pcDNA3.1(+) |
Recombinant DNA reagent | Plasmid: 3HA- CDK9-KKR | This paper | Supplementary file 3 | Progenitor: pcDNA3.1(+) |
Recombinant DNA reagent | Plasmid: 3HA- CDK9-RRK | This paper | Supplementary file 3 | Progenitor: pcDNA3.1(+) |
Recombinant DNA reagent | Plasmid: 3HA -CDK9-RKK | This paper | Supplementary file 3 | Progenitor: pcDNA3.1(+) |
Recombinant DNA reagent | Plasmid: 3HA- CDK9-KRR | This paper | Supplementary file 3 | Progenitor: pcDNA3.1(+) |
Recombinant DNA reagent | Plasmid: 3HA- CDK9-KRK | This paper | Supplementary file 3 | Progenitor: pcDNA3.1(+) |
Recombinant DNA reagent | Plasmid: 3HA- CDK9-RKR | This paper | Supplementary file 3 | Progenitor: pcDNA3.1(+) |
Recombinant DNA reagent | Plasmid: 3HA- CDK9-K0R | This paper | Supplementary file 3 | Progenitor: pcDNA3.1(+) |
Recombinant DNA reagent | Plasmids: 3HA-CDK9-K0R-RXK (X represent mutation position) | This paper | Supplementary file 3 | Progenitor: pcDNA3.1(+) |
Sequence- based reagent | siRNA Library | RiboBio | Supplementary file 1; http://www.ribobio.com/ | |
Sequence- based reagent | ChIP-qPCR Primers | This paper | Supplementary file 2 | |
Sequence- based reagent | siRNA targeting TRIM28 3’UTR:5’- GCTCTGTTCTCTGTCCTGT-3’ | RiboBio | http://www.ribobio.com/ | |
Sequence- based reagent | shRNA targeting Luciferase:5’- ACCGCCTGAAGTCTCTGATTAA-3’ | PMID: 29863470 | N/A | |
Sequence- based reagent | shRNA targeting TRIM28 CDS:5’- CCAGCCAACCAGCGGAAATGTGA-3’ | PMID: 18082607 | N/A | |
Sequence- based reagent | sgRNA targeting Dummyguide (sgNT):5’- ACGGAGGCTAAGCGTCGCAA-3’ | PMID: 25075903 | N/A | Dr. Feng Zhang (Broad Institute of MIT and Harvard) |
Sequence- based reagent | sgRNA targeting TRIM28 CDS:5’- CACCGATTGAGCTGGCAGTCTCGGC-3’ | PMID: 25075903 | N/A | Dr. Feng Zhang (Broad Institute of MIT and Harvard) |
Sequence- based reagent | β-Actin qPCR Forward Primer:5’- GCATGGAGTCCTGTGGCA-3’ | PMID: 27291871 | N/A | |
Sequence- based reagent | β-Actin qPCR Reverse Primer:5’- CAGGAGGAGCAATGATCTTGA-3’ | PMID: 27291871 | N/A | |
Sequence- based reagent | TRIM28 qPCR Forward Primer:5’- CTACTCAAGTGCAGAGCCCC-3’ | This paper | N/A | |
Sequence- based reagent | TRIM28 qPCR Reverse Primer:5’- GGGAAGACCTTGAAGACGGG-3’ | This paper | N/A | |
Sequence- based reagent | HIVTotRNA Forward Primer:5’- CTGGCTAACTAGGGAACCCACTGCT-3’ | PMID: 27291871 | N/A | |
Sequence- based reagent | HIVTotRNA Reverse Primer:5’- GCTTCAGCAAGCCGAGTCCTGCGTC-3’ | PMID: 27535056 | N/A | |
Sequence- based reagent | 1 st round Nest PCR Forward Primer (E00):5’- TAGAAAGAGCAGAAGACAGTGGCAATGA-3’ | PMID: 27434587 | N/A | |
Sequence- based reagent | 1 st round Nest PCR Reverse Primer (ES8B):5’- CACTTCTCCAATTGTCCCTCA-3’ | PMID: 27434587 | N/A | |
Sequence- based reagent | 2nd round Nest PCR Forward Primer (E20):5’- GGGCCACACATGCCTGTGTACCCACAG-3’ | PMID: 27434587 | N/A | |
Sequence- based reagent | 2nd round Nest PCR Reverse Primer (E115):5’- AGAAAAATTCCCCTCCACAATTAA-3’ | PMID: 27434587 | N/A | |
Chemical compound, drug | (+)-JQ-1 | Selleckchem | Cat#S7110 | |
Chemical compound, drug | Vorinostat (SAHA) | Selleckchem | Cat#S1047 | |
Chemical compound, drug | Formaldehyde solution | Sigma-Aldrich | Cat#F8775-25ML | |
Chemical compound, drug | TRIzol Reagent | ThermoFisher | Cat#15596018 | |
Chemical compound, drug | 4',6-Diamidino-2- Phenylindole, Dihydrochloride (DAPI) | ThermoFisher | Cat#D1306 | |
Chemical compound, drug | Cysteamine (MEA) | Sigma-Aldrich | Cat#30070–10G | |
Chemical compound, drug | Glucose Oxidase from Aspergillus niger, Type VII, lyophilized powder, ≥100,000 units/g solid | Sigma-Aldrich | Cat#G2133-250KU | |
Chemical compound, drug | Catalase from bovine liver , lyophilized powder, ≥10,000 units/mg protein | Sigma-Aldrich | Cat#C40-1G | |
Chemical compound, drug | Sodium borohydride (NaBH4) | Sigma-Aldrich | Cat#213462–25G | |
Chemical compound, drug | 16% Paraformaldehyde (formaldehyde) Aqueous Solution | Electron Microscopy Sciences | Cat#15710 | |
Chemical compound, drug | 8% Glutaraldehyde Aqueous Solution | Electron Microscopy Sciences | Cat#16019 | |
Chemical compound, drug | Normal Donkey Serum (NDS) | Jackson ImmunoResearch | Cat#017-000-121 | |
Chemical compound, drug | Triton X-100 | Sigma-Aldrich | Cat#T8787-50ML | |
Chemical compound, drug | Protease Inhibitor Cocktail (PIC) | Sigma-Aldrich | Cat#P8340-1ML | |
Chemical compound, drug | N-Ethylmaleimide (NEM) | Selleckchem | Cat#S3692 | |
Chemical compound, drug | EZview Red Anti-HA Affinity Gel | Sigma-Aldrich | Cat#E6779-1ML | |
Chemical compound, drug | EZview Red Anti- FLAG M2 Affinity Gel | Sigma-Aldrich | Cat#F2426-1ML | |
Chemical compound, drug | Anti-His-tag Agarose | Abcam | Cat#ab1231 | |
Chemical compound, drug | Penicillin-Streptomycin, Liquid | ThermoFisher | Cat#15140122 | |
Chemical compound, drug | L-Glutamine, 200 mM Solution | ThermoFisher | Cat#25030081 | |
Chemical compound, drug | Fetal Bovine Serum (FBS) | ThermoFisher | Cat#10270–106 | |
Chemical compound, drug | Phytohemagglutinin -M (PHA-M) | Sigma-Aldrich | Cat#11082132001 | |
Peptide, recombinant protein | Recombinant Human TNF-α | PeproTech | Cat#300-01A | |
Peptide, recombinant protein | Recombinant Human IL-2 | R&D Systems | Cat#202-IL-500 | |
Peptide, recombinant protein | Recombinant Human SUMO Activating Enzyme E1 (SAE1/UBA2) | R&D Systems | Cat#E-315 | |
Peptide, recombinant protein | Recombinant Human UBE2I/Ubc9 | R&D Systems | Cat#E2-645-100 | |
Peptide, recombinant protein | Recombinant Human CDK9 | Abcam | Cat#ab85603 | |
Peptide, recombinant protein | Recombinant Human SUMO4 | This paper | N/A | |
Peptide, recombinant protein | Recombinant Human TRIM28 | Abcam | Cat#ab131899 | |
Commercial assay or kit
| SUMO Conjugation Reaction Buffer Kit | R&D Systems | Cat#SK-15 | |
Commercial assay or kit | Human Lymphocyte Separation Kit | TBDsciences | Cat#LTS1077 | |
Commercial assay or kit | BD IMag Human CD4 + T Lymphocyte Enrichment Set-DM | BD Biosciences | Cat#557939 | |
Commercial assay or kit | Luciferase Assay System | Promega | Cat#E4550 | |
Commercial assay or kit | SimpleChIP Enzymatic Chromatin IP Kit (Magnetic Beads) | CST | Cat#9003S | |
Commercial assay or kit | TruePrep DNA Library Prep Kit V2 for Illumina | Vazyme | Cat#TD501 | |
Commercial assay or kit | HIV-1 p24 ELISA Kit | Abcam | Cat#ab218268 | |
Commercial assay or kit | ProteoSilver Plus Silver Stain Kit | Sigma-Aldrich | Cat#PROTSIL2 -1KT | |
Commercial assay or kit | CDK9/CyclinK Kinase Enzyme System | Promega | Cat#V4104 | |
Commercial assay or kit | ADP-GloTM Kinase Assay | Promega | Cat#V6903 | |
Commercial assay or kit | Cell Counting Kit-8 | Dojindo | Cat#CK04; Lot#KT793 | |
Commercial assay or kit | Zombie Violet Fixable Viability Kit | BioLegend | Cat#423113; Lot#B256957 | |
Commercial assay or kit | CellTrace CFSE Cell Proliferation Kit - For Flow Cytometry | ThermoFisher | Cat#C34554 | |
Software, algorithm | Prism 5 | GraphPad | https://www.graphpad.com/scientific-software/prism/ | |
Software, algorithm | MEGA 7 | MEGA | https://www.megasoftware.net/ | |
Software, algorithm | Cytoscape (3.6.1) | Cytoscape Consortium | RRID:SCR_015784 | |
Software, algorithm | STRING | Cytoscape Consortium | RRID:SCR_005223 | |
Software, algorithm | MCODE | Cytoscape Consortium | RRID:SCR_015828 | |
Software, algorithm | BD LSRFortessa cell analyzer | BD Biosciences | http://www.bdbiosciences.com/in/instruments/lsr/index.jsp | |
Software, algorithm | FlowJo V10 | Tree Star | https://www.flowjo.com/ | |
Software, algorithm | Odyssey CLX Imager | LI-COR Biosciences | https://www.licor.com/bio/products/imaging_systems/odyssey/ | |
Software, algorithm | Image Studio Lite Ver 4.0 | LI-COR Biosciences | https://www.licor.com/bio/products/software/image_studio_lite/ | |
Software, algorithm | CFX Manager | BIO-RAD | http://www.bio-rad.com/ | |
Software, algorithm | GloMax 96 Microplate Luminometer Software (version 1.9.3) | Promega | https://www.promega.com/resources/software-firmware/detection-instruments-software/promega-branded-instruments/glomax-96-microplate-luminometer/ | |
Software, algorithm | SkanIt SW for Microplate Readers | ThermoFisher | https://www.thermofisher.com/order/catalog/product/5187139?SID=srch-srp-5187139 | |
Software, algorithm | NIS-Elements Advanced Research microscope imaging software | Nikon | https://www.nikoninstruments.com/Products/Software | |
Software, algorithm | PyMOL | Schrödinger | RRID:SCR_000305 | |
Software, algorithm | FastQC | Babraham Institute | RRID:SCR_014583 | |
Software, algorithm | Hisat2 | PMID: 25751142 | RRID:SCR_015530 | |
Software, algorithm | DEGseq | Bioconductor | RRID:SCR_008480 | |
Software , algorithm | gplots | R Foundation | https://www.rdocumentation.org/packages/gplots/versions/3.0.1 | |
Software, algorithm | Bowtie2 | PMID: 22388286 | RRID:SCR_016368 | |
Software, algorithm | Samtools | PMID: 19505943 | RRID:SCR_002105 | |
Software, algorithm | igvtools | Broad Institute | https://software.broadinstitute.org/software/igv/igvtools | |
Software, algorithm | Imaris (Version 9.2) | BITPLANE | RRID:SCR_007370 | |