KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| p53BP1 (phospho-Ser1778) rabbit polyclonal antibody (used for: IF) | Cell Signaling Technology | Cat# 2675; RRID:AB_490917 |
| Actin mouse monoclonal antibody (clone C4) (used for: WB) | Millipore | Cat# MAB1501; RRID:AB_2223041 |
| ARTEMIS (DCLRE1C) rabbit monoclonal antibody (clone D708V) (used for: WB) | Cell Signaling Technology | Cat# 13381; RRID:AB_2798197 |
| mCherry rabbit polyclonal antibody (used for: WB) | GeneTex | Cat# GTX128509 |
| CtIP (RBBP8) rabbit polyclonal antibody (used for: WB) | Bethyl | Cat# A300-488A; RRID:AB_2175262 |
| FEN1 rabbit polyclonal antibody (used for: WB) | Bethyl | Cat# A300-255A; RRID:AB_185550 |
| H2AX rabbit polyclonal antibody (used for: ChIP) | Millipore | Cat# 07-627; RRID:AB_2233033 |
| γH2AX (phospho-Ser139) mouse monoclonal antibody (clone JBW301) (used for: IF) | Millipore | Cat# 05-636; RRID:AB_309864 |
| γH2AX (phospho-Ser139) rabbit polyclonal antibody (used for: ChIP) | Millipore | Cat# 07-164; RRID:AB_310406 |
| KAP-1 (TRIM28) rabbit polyclonal antibody (used for: WB) | Bethyl | Cat# A300-274A; RRID:AB_185559 |
| Lamin B1 rabbit polyclonal antibody (used for: WB) | Abcam | Cat# ab16048; RRID:AB_443298 |
| DNA ligase 3 (LIG3, DNL3) rabbit polyclonal antibody (used for: WB) | Bethyl | Cat# A301-636A; RRID:AB_1210932 |
| MRE11 rabbit polyclonal antibody (used for: WB) | Bethyl | Cat# A303-998A; RRID:AB_2620347 |
| MUS81 mouse monoclonal antibody (clone MTA30 2G10/3 (used for: WB) | Abcam | Cat# ab14387; RRID:AB_301167 |
| PNKP (PNK1) rabbit polyclonal antibody (used for: WB) | Bethyl | Cat# A300-257A; RRID:AB_263356 |
| S9.6 mouse monoclonal antibody (used for: DRIP, Slot-blot) | Gromak Lab | N/A; RRID:AB_2810829 |
| ssDNA (single stranded DNA) mouse monoclonal antibody (clone 16-19) (used for: Slot-blot) | Millipore | Cat# MAB3034; RRID:AB_94645 |
| SETX (Senataxin) rabbit polyclonal antibody (used for: WB) | Bethyl | Cat# A301-104A; RRID:AB_873128 |
| SETX (Senataxin) rabbit polyclonal antibody (used for: ChIP) | Novus | NB100-57542; RRID:AB_922411 |
| TDP1 mouse polyclonal antibody (used for: WB) | Abnova Corporation | Cat# H00055775-A01; RRID:AB_461513 |
| aTubulin mouse monoclonal antibody (clone B-5-1-2) (used for: WB) | Sigma-Aldrich | Cat# T5168; RRID:AB_477579 |
| XPF (ERCC4) rabbit polyclonal antibody (used for: WB) | Bethyl | Cat# A301-315A; RRID:AB_938089 |
| XPF (ERCC4) rabbit polyclonal antibody (used for: ChIP and WB) | Abcam | Cat# ab76948; RRID:AB_1524575; Lot#GR172751 |
| XPG (ERCC5) rabbit polyclonal antibody (used for: WB) | Bethyl | Cat# A301-484A; RRID:AB_999684 |
| XRCC1 rabbit polyclonal antibody (used for: WB) | Bethyl | Cat# A300-065A; RRID:AB_2218477 |
| Donkey anti-mouse secondary antibody, Alexa Fluor 488 (used for: IF) | ThermoFisher Scientific | Cat# A-21202; RRID:AB_141607 |
| Goat anti-rabbit secondary antibody, Alexa Fluor 594 (used for: IF) | ThermoFisher Scientific | Cat# A-11037; RRID:AB_2534095 |
| Goat anti-mouse secondary antibody, Alexa Fluor 594 (used for: IF) | ThermoFisher Scientific | Cat# A-11032; RRID:AB_2534091 |
| Goat anti-rabbit secondary antibody, Alexa Fluor 647 (used for: IF) | ThermoFisher Scientific | Cat# A-21245; RRID:AB_2535813 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Bortezomib (PS-341) | Selleckchem | Cat# S1013; CAS: 179324-69-7 |
| CPT [(S)-(+)-Camptothecin] | Sigma-Aldrich | Cat# C9911; CAS: 7689-03-4 |
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
| Dharmafect 4 transfection reagent | Dharmacon | Cat# T-2004 |
| Doxycycline hyclate | Sigma-Aldrich | Cat# D9891; CAS 24390-14-5 |
| FLV (Flavopiridol hydrochloride hydrate) | Sigma-Aldrich | Cat# F3055 |
| Halt Protease & Phosphatase Inhibitor Cocktail | ThermoFisher Scientific | Cat# 1861281 |
| MG132 (Z-Leu-Leu-Leu-al) | Sigma-Aldrich | Cat# C9911; CAS: 133407-82-6 |
| Myricetin | Sigma-Aldrich | Cat# M6760; CAS: 529-44-2 |
| Poly-L-lysine solution | Sigma-Aldrich | Cat# P4832 |
| Proteinase K | Sigma-Aldrich | Cat# 03115828001 |
| RNase H | NEB | Cat# M0297 |
| Critical Commercial Assays | ||
| CellTiter-Blue cell viability assay | Promega | Cat# G8080 |
| Click-iT EdU Alexa Fluor 647 Imaging Kit | ThermoFisher Scientific | Cat# C10340 |
| Click-iT RNA Alexa Fluor 488 Imaging Kit | ThermoFisher Scientific | Cat# C10329 |
| CometAssay Kit | Trevigen | Cat# 4250-050-K |
| Experimental Models: Cell Lines | ||
| Human: WI38 hTERT cells | Carl Mann laboratory (Jeanblanc et al., 2012) | N/A |
| Human: XP2Y0 (XPF-deficient) cells | Orlando Schärer laboratory (Staresincic et al., 2009) | N/A |
| Human: XP2Y0 + XPF WT cells | Orlando Schärer laboratory (Staresincic et al., 2009) | N/A |
| Human: XP2Y0 + XPF-D676A (nuclease-dead) cells | Orlando Schärer laboratory (Staresincic et al., 2009) | N/A |
| Human: HCT116 cells | Yves Pommier laboratory (Al Abo et al., 2017) | N/A |
| Human: HCT116 TDP1 KO cells | Yves Pommier laboratory (Al Abo et al., 2017) | N/A |
| Human: U2OS cells inducible for mCherry | Patrick Calsou laboratory (Britton et al., 2014) | N/A |
| Human: U2OS cells inducible for mCherry-RNH1 | Patrick Calsou laboratory (Britton et al., 2014) | N/A |
| Oligonucleotides | ||
| AQR (Aquarius) (human) individual siRNA | Dharmacon | Cat# D-022214-03 |
| ARTEMIS (DCLRE1C) (human) SMARTpool siRNA | Dharmacon | Cat# M-004269-02 |
| CtIP (RBBP8) (human) SMARTpool siRNA | Dharmacon | Cat# M-011376-00 |
| DNA ligase 3 (LIG3, DNL3) (human) SMARTpool siRNA | Dharmacon | Cat# M-009227-02 |
| FEN1 (human) SMARTpool siRNA | Dharmacon | Cat# M-010344-01 |
| LUC (Luciferase GL3 Duplex) siRNA | Dharmacon | Cat# D-001400-01 |
| MRE11 (human) SMARTpool siRNA | Dharmacon | Cat# M-009271-01 |
| MUS81 (human) SMARTpool siRNA | Dharmacon | Cat# L-016143-01 |
| PNKP (human) SMARTpool siRNA | Dharmacon | Cat# M-006783-02 |
| RAD52 (human) SMARTpool siRNA | Dharmacon | Cat# M-011760-01 |
| SETX (Senataxin) (human) siRNA: 5’-UUGGAGUAGUU GAUACCCGAAdTdT-3’ | This paper | N/A |
| TDP1 (human) SMARTpool siRNA | Dharmacon | Cat# M-016112-01 |
| XPF (ERCC4) (human) SMARTpool siRNA | Dharmacon | Cat# M-019946-00 |
| XPG (ERCC5) (human) SMARTpool siRNA | Dharmacon | Cat# M-006626-01 |
| XRCC1 (human) SMARTpool siRNA | Dharmacon | Cat# M-009394-01 |
| Nontargeting control siRNA | Eurogentec | Cat# SR-CL000-005 |
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
| ssDNA: CGGTGTGAATCAGAC (used for DNA/RNA hybrid competition) | Sigma-Aldrich | N/A |
| ssRNA: GUCUGAUUCACACCG (used for DNA/RNA hybrid competition) | Dharmacon | N/A |
| See Table S1 for primers used in this study. | ||
| Software and Algorithms | ||
| Columbus software (versions 2.5.0 and 2.8.2) | PerkinElmer | N/A |
| GraphPad Prism 6.0 | GraphPad Prism | https://www.graphpad.com/; RRID:SCR_002798 |
| Harmony software (versions 4.1 and 4.8) | PerkinElmer | N/A |
| ImageJ software (versions 1.48, 1.51, and 1.52) | National Institutes of Health | https://imagej.nih.gov/ij/; RRID:SCR_003070 |
| OpenComet (version 1.3.1) | OpenComet Software | http://www.cometbio.org |
| Other | ||
| AxioObserver Z1 fluorescence microscope | ZEISS | https://www.zeiss.com/corporate/int/home.html |
| LSM 780 confocal microscope | ZEISS | https://www.zeiss.com/corporate/int/home.html |
| CLARIOstar microplate reader | BMG Labtech | https://www.bmglabtech.com |
| ChemiDoc MP Imaging System | Bio-Rad | http://www.bio-rad.com |
| Operetta High-Content Imaging System | PerkinElmer | https://www.perkinelmer.com |
| Operetta CLS High-Content Imaging System | PerkinElmer | https://www.perkinelmer.com |
| CellCarrier 96-well | PerkinElmer | Cat# 6005550 |
| Lab-Tek RS chamber slides | ThermoFisher Scientific | Cat# 154526K |