KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-XPA | Santa Cruz | sc-853 |
| Rabbit anti-XPA | Genetex | GTX103168 |
| Rabbit anti-XPB | Santa Cruz | sc-293 |
| Rabbit anti-XPC | Bethyl | A301-112A |
| Mouse anti-XPD | Abcam | ab54676 |
| Mouse anti-XPF | Santa Cruz | sc-136153 |
| Mouse anti-XPG | Abcam | ab46 |
| Rabbit anti-XPG | Bethyl | A301-484A |
| Mouse anti-Cyclin H (2D4) | ThermoScientific | MA3-025 |
| Rabbit anti-RAD18 | Bethyl | A301-340A |
| Mouse anti-PCNA | Abcam | ab29 |
| Mouse anti-GTF2H1 | Sigma-Aldrich | 1F12-1B5 |
| Rabbit anti-GTF2H1 | Novus Biologicals | NBP-38556 |
| Rat anti-HA (3F10) | Roche | 12158167001 |
| Mouse anti-FLAG (M2) | Sigma-Aldrich | F1804 |
| Rabbit anti-HLTF | Santa Cruz | sc-366563 |
| Rabbit anti-HLTF | Abcam | ab155031 |
| Rabbit anti-HLTF | ThermoScientific | PA5-79371 |
| Mouse anti-6-4PP (64M2) | Cosmo Bio | CAC-NM-DND-002 |
| Mouse anti-CPD (TDM2) | Cosmo Bio | CAC-NM-DND-001 |
| Rabbit anti-ERCCI | Abcam | ab129267 |
| Mouse anti-XAB2 | Santa Cruz | sc-271037 |
| Mouse anti-Tubulin (B512) | Sigma-Aldrich | T5168 |
| Goat anti-Ku70 | Santa Cruz | sc1487 |
| Mouse anti-GAPDH | Abcam | ab8245 |
| Mouse anti-YH2AX | Millipore | JWB301 |
| Rabbit anti-GFP | Abcam | ab290 |
| Rabbit anti-POLDI | Abcam | ab126407 |
| Mouse anti-SMARCALI | Santa Cruz | sc-376377 |
| Rabbit anti-ZRANB3 | Proteintech Group | 23111-1-AP |
| Rabbit anti-RFC1 | Invitrogen | PA5-35965 |
| Goat anti-rabbit CF™ IRDye 770 | Sigma-Aldrich | sab4600215 |
| Goat anti-rabbit CF™ IRDye 680 | Sigma-Aldrich | sab4600200 |
| Goat anti-mouse CF™ IRDye 770 | Sigma-Aldrich | sab4600214 |
| Goat anti-mouse CF™ IRDye 680 | Sigma-Aldrich | sab4600199 |
| Donkey-anti-goat CF™ IRDye 770 | Sigma-Aldrich | sab4600375 |
| Goat anti-rat CF™ IRDye 770 | Sigma-Aldrich | sab4600479 |
| Goat anti-rabbit AlexaFluor® 488 | Invitrogen | A11034 |
| Goat anti-mouse AlexaFluor® 488 | Invitrogen | A11001 |
| Goat anti-rabbit AlexaFluor® 594 | Invitrogen | A11012 |
| Goat anti-mouse AlexaFluor® 594 | Invitrogen | A11032 |
| Goat anti-rat AlexaFluor® 555 | Invitrogen | A21434 |
| Donkey anti-rabbit AlexaFluor® 647 | Invitrogen | A31573 |
| Duolink® anti-Mouse MINUS PLA® Probe | Sigma-Aldrich | DU092004 |
| Duolink® anti-Rabbit PLUS PLA® Probe | Sigma-Aldrich | DU092005 |
| Bacterial and virus strains | ||
| One Shot™ Top1G Chemically competent cells | Invitrogen | C4040-06 |
| Chemicals, peptides, and recombinant proteins | ||
| Triptolide | Sigma-Aldrich | T3652 |
| Spironolactone | Sigma-Aldrich | S3378 |
| Hydroxyurea | Sigma-Aldrich | H8627 |
| Cytarabine | Sigma-Aldrich | C3350000 |
| Puromycin | InvivoGen | ant-pr-1 |
| 5-ethynyl-2'-deoxyuridine (EdU) | Invitrogen | A10044 |
| 5-fluoro-2’-deoxyuridine (FuDR) | Sigma-Aldrich | 856657 |
| Lipofectamine™ RNAiMAX | Invitrogen | 13778500 |
| DMEM without lysine and arginine | AthenaES | 0420 |
| Dialyzed fetal calf serum | Gibco | 26400044 |
| [12C6]-lysine | Silantes | 211004102 |
| [12C6,14N4]-arginine | Silantes | 201003902 |
| [13C6]-lysine | Cambridge Isotope Laboratories | CNLM-291-H-1 |
| [13C6,15N4]-arginine | Cambridge Isotope Laboratories | CNLM-539-H-1 |
| FuGENE® 6 Transfection Reagent | Promega | E2691 |
| X-tremeGENE® 9 DNA transfection reagent | Roche | 6365787001 |
| AlamarBlue® | Invitrogen | DAL1025 |
| 2x Laemmli sample buffer | Sigma-Aldrich | S3401 |
| Benzonase® Nuclease | Novagen/Millipore | 70664 |
| Atto 594 Azide | Atto Tec | AD594-105 |
| 4',6-diamidino-2-phenylindole (DAPI) | Sigma-Aldrich | D9542 |
| Aqua-Poly/Mount | Polysciences, Inc. | 18606-20 |
| RNase A | ThermoScientific | EN0531 |
| RNase T1 | ThermoScientific | EN0541 |
| Proteinase K | ThermoScientific | EO0491 |
| Critical commercial assays | ||
| Tyramide Signal Amplification kit with AlexaFluor™ 488 Tyramide Reagent | Invitrogen | B40932 |
| Duolink® In Situ Detection Reagents Red | Sigma-Aldrich | DUO92008 |
| Pierce™ BCA Protein Assay | ThermoScientific | 23225 |
| Deposited data | ||
| Experimental models: cell lines | ||
| U2OS | ATCC | |
| U2OS CPD photolyase-mCherry | (Steurer et al., 2019) | |
| U2OS XPF KO | (Sabatella et al., 2018) | |
| U2OS XPF KO + GFP-XPF | (Sabatella et al., 2018) | |
| XPCS2BA-sv40 + XPB-GFP | (Hoogstraten et al., 2002) | |
| XP4PA-sv40 + XPC-GFP | (Ribeiro-Silva et al., 2018) | |
| XPCS1RO-sv40 + XPG-GFP | (Zotter et al., 2006) | |
| MRC5-sv40 | ATCC | |
| Xpb-YFP KI MDFs | (Giglia-Mari et al., 2009) | |
| Xpb-YFP KI MDFs Xpc−/− | (Giglia-Mari et al., 2009) | |
| Xpb-YFP KI MDFs Xpg−/− | (Giglia-Mari et al., 2009) | |
| XP186LV | (Wienholz et al., 2017) | |
| C3RO-hTERT | ||
| C5RO-hTERT | ||
| VH10-hTERT | ||
| XP25RO-hTERT | ||
| U2OS GFP-HLTF KI | This paper | N/A |
| U2OS GFP-HLTF KI XPG KO | This paper | N/A |
| U2OS GFP-HLTF KI XPG KO + wt HA-XPG | This paper | N/A |
| U2OS GFP-HLTF KI XPG KO + EZ91A HA-XPG | This paper | N/A |
| U2OS HLTF KO A | This paper | N/A |
| U2OS HLTF KO B | This paper | N/A |
| HEK293T | ||
| Oligonucleotides | ||
| sgHLTF (5’-CCATGTCCTGGATGTTCAAG-3’) | Integrated DNA technologies | N/A |
| sgXPG (5’-GCTGGAGTGCTCCGGGCGGC-3’) | Integrated DNA technologies | N/A |
| siCTRL | Horizon Discovery | N/A |
| siHLTF A A (5’-GGUGCUUUGGCCUAUAUCAUU-3’) | Horizon Discovery | N/A |
| siHLTF B (5’-GGAAACAAUACCAGUGAAAUU-3’) | Horizon Discovery | N/A |
| siXPF (5’-AAGACGAGCUCACGAGUAUUU-3’) | Horizon Discovery | N/A |
| siXPC (5’-CUGGAGUUUGAGACAUAUCUU-3’) | Horizon Discovery | N/A |
| siXPG (SmartPool) | Horizon Discovery | M-006626-00 |
| siGTF2H1 (SmartPool) | Horizon Discovery | L-010924-00 |
| siRAD18 (5’-GCUCUCUGAUCGUGAUUUAUU-3’) | Horizon Discovery | N/A |
| siRFCI | ThermoScientific | M-009290-01 |
| siSMARCALI (5’-GCUCUCUGAUCGUGAUUUAUU-3’) | Horizon Discovery | N/A |
| siZRANB3 (5'-GAUCAGACAUCACACGAUUU-3') | Horizon Discovery | N/A |
| HIRAN mutant primer Forward (5’-CAACGAGAT CCT GCTGCCCCTTAT GATAAG-3') | Integrated DNA Technologies | N/A |
| HIRAN mutant primer Reverse (5’-CTTATCATAAGGGGCAGCAGGATCTCGTTG-3’) | Integrated DNA Technologies | N/A |
| RING mutant primer Forward (5’-GGTT CAGAT GAGGAAT CTGCAA1 1 1GCCTGGATTC-3’) | Integrated DNA Technologies | N/A |
| RING mutant primer Reverse (5’-GAATCCAGGCAAATTGCAGATTCCTCATCTGAACC-3’) | Integrated DNA Technologies | N/A |
| ATPase mutant primer Forward (: 5’-AGAGTGATCCTGGCTGCAGGACATGCCATACG-3’) | Integrated DNA Technologies | N/A |
| ATPase mutant primer Reverse (5’-CGTATGGCATGTCCTGCAGCCAGGATCACTCT-3’) | Integrated DNA Technologies | N/A |
| Recombinant DNA | ||
| pLenti-CMV-Puro | Addgene | 1Z452 |
| pLenti-CRISPRv2 | Addgene | 52961 |
| pLenti-CMV-Puro-GFP-HLTF | This paper | N/A |
| pLenti-CMV-Puro-Flag-HLTF | This paper | N/A |
| pWPXL-EF1 a-XPG (WT) | (Staresincic et al., 2009) | N/A |
| pWPXL-EF1 a-XPG (EZ91A) | (Staresincic et al., 2009) | N/A |
| pEGFP-POLK | (Ogi et al., 2010) | N/A |
| Software and algorithms | ||
| MaxQuant software suite (version 1.5.3.8) | (Cox et al., 2011) | N/A |
| Fiji ImageJ | N/A | |
| Prism GraphPad (version 9.0) | GraphPad software Inc. | N/A |
| Leica LAS | N/A | |
| LAS AF (version 27.4.10100) | Leica Microsystems | |
| Other | ||
| TUV lamp (UV-C) | Phillips | N/A |
| Isopore membrane filter 5 μm pores TMTP | Millipore | TMTP04Z00 |
| Isopore membrane filter 8 μm pores TETP | Millipore | TETP04Z00 |
| Glomax® Multimode reader | Promega | |
| Bioruptor Sonicator | Diagenode | |
| Soniprep 150 | MSE | |
| GFP-Trap-A® agarose bead slurry | ChromoTek | gta-100 |
| Agarose binding control beads | ChromoTek | bab-20 |
| Mini-PROTEAN TGX™ Precast Protein Gels | BioRad | 456-1084 |
| Orbitrap Fusion Tribid mass spectrometer | ThermoScientific | |