KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| FANCI | Bethyl | A301-254A; RRID:AB_890616 |
| FANCA | Bethyl | A301-980A; RRID:AB_1547945 |
| FANCD2 | Abcam | ab108928; RRID:AB_10862535 |
| Myc tag | Cell Signaling Technology | 2278; RRID:AB_490778 |
| Flag tag | Sigma | F3165; RRID:AB_259529 |
| Flag | Cell signaling | 14793S; RRID:AB_2572291 |
| β-Actin | Sigma | A5316; RRID:AB_476743 |
| eIF4G | Santa Cruz | Sc-133155; RRID:AB_2095748 |
| HIV-1 p24 | Abcam | Ab9071; RRID:AB_306981 |
| β-Tubulin | ABclonal | A12289; RRID:AB_2861647 |
| Phospho-Histone H2AX-S139 Rabbit pAb | ABclonal | AP0099; RRID:AB_2771168 |
| Anti-gamma H2A.X (phospho S139) antibody [3F2] | Abcam | ab22551; RRID:AB_447150 |
| RPA1 | Proteintech | 67973-1-Ig |
| FITC-labeled Goat Anti-Rabbit IgG (H + L) | Beyotime | A0562 |
| Cy3-labeled Goat Anti-Rabbit IgG (H + L) | Beyotime | A0516 |
| Anti-Mouse IgG (whole molecule)–TRITC, antibody produced in goat | Sigma | T5393 |
| FAN1 Polyclonal Antibody | Proteintech | 17600-1-AP; RRID:AB_1059801 |
| REV1 Rabbit pAb | ABclonal | A8493; RRID:AB_2771985 |
| Anti-SLX4 | Abcam | ab169114 |
| SNM1A Rabbit pAb | ABclonal | A14312; RRID:AB_2761176 |
| Ku70 Rabbit pAb | ABclonal | A7330; RRID:AB_2767867 |
| FEN1 Polyclonal Antibody | Proteintech | 14768-1-AP; RRID:AB_2102780 |
| LRS antibody | Abcam | ab31534; RRID:AB_776011 |
| Bacterial and virus strains | ||
| Trans10 Chemically Competent Cell | Transgen Biotech | CD101-01 |
| HIV-1 (NL4.3) | NIH AIDS Reagent Program | 114 |
| Chemicals, peptides, and recombinant proteins | ||
| DNase I | Sigma | D5025 |
| Benzonase | Sigma | E1014 |
| Puromycin | Sigma | P9620 |
| RNase A | Thermo Fisher Scientific | AM2271 |
| Lipofectamine 2000 | Thermo Fisher Scientific | 11668019 |
| TRIzol Reagent | Thermo Fisher Scientific | 15596018 |
| ANTI-FLAG M2 Magnetic Beads | Sigma | M8823 |
| passive lysis buffer | Promega | E1941 |
| Aphidicolin | Abacm | ab142400 |
| Dimethyl sulfoxide (DMSO) ACS | AMRESCO | 0231-500ML |
| Propidium iodide | Sigma | P4170 |
| Paraformaldehyde,4% | Solarbio | P1110 |
| DAPI Staining Solution | Beyotime | C1005 |
| Critical commercial assays | ||
| Luciferase Assay System | Promega | E1501 |
| SuperReal PreMix Plus (SYBR Green) | Tiangen | FP205 |
| DNeasy Blood & Tissue Kit | Qiagen | 69506 |
| Experimental models: Cell lines | ||
| HEK293T | ATCC | CRL-11268 |
| TZM-bl | NIH AIDS Reagent Program | 8129 |
| MT-4 | NIH AIDS Reagent Program | 120 |
| GM6914 | Coriell | GM6914 |
| 293A | Invitrogen | R70507 |
| Oligonucleotides | ||
| qGAPDH-F | This study | TCGGAGTCAACGGATTTG |
| qGAPDH-R | This study | GCATCGCCCCACTTGATT |
| qLate RT product-F | This study | TGTGTGCCCGTCTGTTGTG |
| qLate RT product-R | This study | GAGTCCTGCGTCGAGA |
| qInt-1F | This study | GCCTCCCAAAGTGCTGGGATTACAG |
| qInt-1R | This study | GTTCCTGCTATGTCACTTCC |
| qInt-2F | This study | TTAAGCCTCAATAAAGCTTGCC |
| qInt-2R | This study | GTTCGGGCGCCACTGCTAGA |
| q2-LTR-F | This study | CCCTCAGACCCTTTTAGTCAGTG |
| q2-LTR-R | This study | TGGTGTGTAGTTCTGCCAATCA |
| qMito-F | This study | ACCCACTCCCTCTTAGCCAATATT |
| qMito-R | This study | GTAGGGCTAGGCCCACCG |
| qFAN1-F | This study | GTGGCCCCAGGAAGAAGAAA |
| qFAN1-R | This study | AATCACTTTGGCCAGGGGTT |
| qREV1-F | This study | CTGGTCCCTGGCGAGGGCACTGG |
| qREV1-R | This study | TCTGCATAGCAGCATCTGATCG |
| qPOLA-F | This study | GGACCAACACATCTAGCCTGGA |
| qPOLA-R | This study | GGTCTGGTTTCAAAGCCATTGCC |
| qPOLB-F | This study | TGCAGAGTCCAGTGGTGACATG |
| qPOLB-R | This study | ATGAACCTTTTGTAACTGCTCCAC |
| qPOLD1-F | This study | ACTACACGGGAGCCACTGTCAT |
| qPOLD1-R | This study | GCGTGGTGTAACACAGGTTGTG |
| qPOLD2-F | This study | ACTGACCCGTTCATCTTCCCAG |
| qPOLD2-R | This study | CAACAGCACTGTCTGGTCCTCA |
| qPOLD4-F | This study | CTGCTGAGGCAGTTTGACCTGG |
| qPOLD4-R | This study | TCTTCAGCACCTGCCACACCTC |
| qPOLE-F | This study | ACGCTGGAAGAGGTGTATGGCT |
| qPOLE-R | This study | GGAACGGTTCTCAGAGATGAGC |
| qPOLG-F | This study | AGATGGAGAACTTGCGAGCTGC |
| qPOLG-R | This study | CACGTCGTTGTAAGGTCCATTGC |
| qPOLH-F | This study | GTGCCAGTTACCAGCTCAGA |
| qPOLH-R | This study | AGGTAATGAGGGCTTGGATG |
| qPOLI-F | This study | CTACTTCACGCTCTGGCAAGCA |
| qPOLI-R | This study | GTGGTATCTAGTGGAGACTCCC |
| qPOLK-F | This study | CCAGACATCACAACCATTCC |
| qPOLK-R | This study | TCAAGGCTTCCAGACTGATG |
| qPOLL-F | This study | CCATAAGCCTGTCACCTCGTAC |
| qPOLL-R | This study | GCTCTCACTGATATGGTCCAGC |
| qPOLM-F | This study | TGTGAGGAGGTGGAGAGAGTTC |
| qPOLM-R | This study | TCGGAGGTCATCTAAGGTTCGC |
| qPOLN-F | This study | CGAGCAATAACCAGCTTCGAGAG |
| qPOLN-R | This study | GGATGAAGGTCTCGCAGAGCAT |
| qPOLQ-F | This study | CTTGTGGCATCTCCTTGGAGCA |
| qPOLQ-R | This study | AATCCCTTGGCTGGTCTCCATC |
| qREV3L-F | This study | GTCTGAGACTATTTACCAGGAACC |
| qREV3L-R | This study | CCTTCCAAGGAAAAGTCTCCCTC |
| siNC | This study | UAAGGCUAUGAAGAGAUAC |
| siPOLA | This study | GCACGCAAUAAAGACAAGA |
| siPOLB | This study | GCAGCAUCUGUUAUAGCAA |
| siPOLD1 | This study | CCCUCAAGGUACAAACAUU |
| siPOLD2 | This study | CCAUUGAUGGAGUCAGAUU |
| siPOLD4 | This study | CCUCAGGACAGAAGCGAGA |
| siPOLE | This study | CGGAAGCAGAUUUAAGGUG |
| siPOLG | This study | GGUGCACAGACUUUAUGUA |
| siPOLH | This study | GCUCGUGCAUUUGGAGUCA |
| siPOLI | This study | GGAAAUUAUGAUGUGAUGA |
| siPOLK | This study | CCAAUAGACAAGCUGUGAU |
| siPOLL | This study | GGGAGAAGAAGCAGAAGAG |
| siPOLM | This study | GCGACACAUGUUGUGAUGG |
| siPOLN | This study | GCACCCAAUUCAGAUUACU |
| siPOLQ | This study | GGAAUGCCAUUUUCAAUUA |
| siREV3L | This study | AUGAGUAUGGAUCAUAUAC |
| siREV1 | This study | AUCGGUGGAAUCGGUUUGG |
| FANCA sgRNA-1 | This study | AGACGCATACTGACCACTCG |
| FANCA sgRNA-2 | This study | CCTCCACTCACAAGATCGTG |
| FANCA sgRNA-3 | This study | GACACACAGAACCTTCCGAG |
| FANCD2 sgRNA-1 | This study | AGTTGACTGACAATGAGTCG |
| FANCD2 sgRNA-2 | This study | TCATAGAGGCCAGCTAAACA |
| FANCD2 sgRNA-3 | This study | TTGACAATAGGTGTTTGACC |
| FANCI sgRNA-1 | This study | GTATCCAGTTGGTGGAATCG |
| FANCI sgRNA-2 | This study | AAATGAAACCAAGTTCTACG |
| FANCI sgRNA-3 | This study | TATGACTGTATTCTTATACC |
| FAN1 sgRNA-1 | This study | TGCCGGTTTAAGTCATATCT |
| FAN1 sgRNA-2 | This study | CTGATTGATAAGCTTCTACG |
| FAN1 sgRNA-3 | This study | GACTTCGTTCAAGTGGATCC |
| REV1 sgRNA-1 | This study | GCGAGCTGAAAATGATGGCT |
| REV1 sgRNA-2 | This study | AATTCGACCAGAATGGATTG |
| REV1 sgRNA-3 | This study | AAACTAATGATGTTGCATGG |
| SNM1A sgRNA-1 | This study | ACGAAGACCATCTTTCCTCA |
| SNM1A sgRNA-2 | This study | GAAGTGCCCCTTGGAAATGC |
| SNM1A sgRNA-3 | This study | AGGTGTCTGCCCTATCAATG |
| SLX4 sgRNA-1 | This study | ACGGAGGTTTCTTCTCTGCA |
| SLX4 sgRNA-2 | This study | CTGCGCTAGCTTTTTCCAAA |
| SLX4 sgRNA-3 | This study | CGGTTCACTTGCTTGCCATT |
| Ku70 sgRNA-1 | This study | CGAGGGCGATGAAGAAGCAG |
| Ku70 sgRNA-2 | This study | TTCCAAGACATGATGGGCCA |
| Ku70 sgRNA-3 | This study | TGATCGAGATCTCTTGGCTG |
| FEN1 sgRNA-1 | This study | GCCGTTCTCCATCATGCGAA |
| FEN1 sgRNA-2 | This study | AAGCCGCCACAGCTCAAGTC |
| FEN1 sgRNA-3 | This study | CTTGCCATCAAAGACATACA |
| pCDH-CMV-MCS-EF1-Puro-IN-F | This study | GGATTCCTGGACGGCATTGACAAGGC |
| pCDH-CMV-MCS-EF1-Puro-IN-R | This study | TTAGTCCTCATCTTGACGAGAGGC |
| pCMV-HF-INΔCTD-F | This study | ATGCAGAAGCAGATCACCAAGATCC |
| pCMV-HF-INΔCTD-R | This study | TTAGTCCTCATCTTGACGAGAGGC |
| pCMV-Myc-FAN1-F | This study | ATGATGTCAGAAGGGAAACCT |
| pCMV-Myc-FAN1-R | This study | TTAGCTAAGGCTTTGGCTCTTAGC |
| pCMV-Myc-FAN1 UBZ MUT C44A_C47A | This study | CCACCTGCTAAACTTGCCGCACCCGTTGCAAGTAAAATGGTGCCTAGATATG |
| pCMV-Myc-FAN1 NUC MUT E975A K977A | This study | CACTTTAAGCTGGTGGCAGTTGCAGGCCCCAATGATCGTC |
| pCMV-Myc-REV1-F | This study | ATGAGGCGAGGTGGATGGAGG |
| pCMV-Myc-REV1-R | This study | TTATGTAACTTTTAATGTGCTTC |
| pCMV-Myc-REV1 ΔCTD-R | This study | ATTCTTTGGCACAGATGCGCTGGCTCA |
| pCMV-Myc-FAN1-NGG-MUT-F-1 | This study | AGTAAAATGGTGCCAAGATATGACTTAA |
| pCMV-Myc-FAN1-NGG-MUT-R-1 | This study | AGGTGCCGGTTTAAGTCATATCTTGGCACC |
| pCMV-Myc-FAN1-NGG-MUT-F-2 | This study | TCCTGACAAAAAAAGGCCACGTAG |
| pCMV-Myc-FAN1-NGG-MUT-R-2 | This study | ATAAGCTTCTACGTGGCCTTTTTTTG |
| pCMV-Myc-FAN1-NGG-MUT-F-3 | This study | GTTCAAGTGGATCCTGGGCAGGTT |
| pCMV-Myc-FAN1-NGG-MUT-R-3 | This study | TTTATTAAGCCAACCTGCCCAGGATC |
| pCMV-Myc-REV1-NGG-MUT-F-1 | This study | GAAAATGATGGCTGCGAAACA |
| pCMV-Myc-REV1-NGG-MUT-R-1 | This study | CCCACCCCATGTTTCTCAGCCAT |
| pCMV-Myc-REV1-NGG-MUT-F-2 | This study | TTCGACCAGAATGGATTGTAGAAAGC |
| pCMV-Myc-REV1-NGG-MUT-R-2 | This study | CCAGCTTTGATGCTTTCTACAATC |
| pCMV-Myc-REV1-NGG-MUT-F-3 | This study | AACTAATGATGTTGCATGGCGGTCAATA |
| pCMV-Myc-REV1-NGG-MUT-R-3 | This study | GAATAATATACATGGTATTGACCGCCAT |
| pLvx-EF1-IRES-Neo-FANCD2-NGG-MUT-F | This study | GTGATGAAATCAACATACCACGACT |
| pLvx-EF1-IRES-Neo-FANCD2-NGG-MUT-R | This study | ACTGACAATGAGTCGTGGTATGTTG |
| pLvx-EF1-IRES-Neo-FANCA-NGG-MUT-F | This study | GTTGCCTCTAGCGTCGGACAGATCT |
| pLvx-EF1-IRES-Neo-FANCA-NGG-MUT-R | This study | AGCCGTGCAGATCTGTCCGACGCTAG |
| pLvx-EF1-IRES-Neo-FANCI-NGG-MUT-F | This study | TATACACTTGCTGTATCCAGTTGGTG |
| pLvx-EF1-IRES-Neo-FANCI-NGG-MUT-R | This study | TTCCACCAACTGGATACAGCAAGTG |
| Recombinant DNA | ||
| pNCA-Luc | Addgene | 67793 |
| pNL4-3 | NIH AIDS Reagent Program | 114 |
| pNL4.3-Luc | NIH AIDS Reagent Program | 3418 |
| pMLV-luc | This study | N/A |
| lentiCRISPR v2 | Addgene | 52961 |
| pCMVdeltaR8.2 | Addgene | 12263 |
| pMD2.G | Addgene | 12259 |
| pCMV-HF | N/A | PMID: 21876179 |
| pCMV-Myc | TAKARA | 635689 |
| pLvx-IRES-Neo | TAKARA | 632181 |
| pLvx-EF1-IRES-Neo | This study | N/A |
| pCMV-Intron | This study | N/A |
| pNL4.3-mCherrey | This study | N/A |
| pCMV-HF-IN | This study | N/A |
| pCDH-CMV-MCS-EF1-Puro-IN | This study | N/A |
| pCMV-HF-INΔCTD | This study | N/A |
| pLvx-EF1-IRES-Neo-FANCA | This study | N/A |
| pLvx-EF1-IRES-Neo-FANCD2 | This study | N/A |
| pLvx-EF1-IRES-Neo-FANCI | This study | N/A |
| pCMV-Myc-FAN1 | This study | N/A |
| pCMV-Myc-REV1 | This study | N/A |
| pCMV-Myc-FAN1UBZmut | This study | N/A |
| pCMV-Myc-FAN1NUCmut | This study | N/A |
| pCMV-Myc-REV1ΔCTD | This study | N/A |
| Software and algorithms | ||
| GraphPad Prism 8 | GraphPad software | N/A |
| FlowJo V10 | FLOWJO software | N/A |
| Image J | Image J | N/A |