KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-53BP1 | Novus Biologicals | Cat# NB100-305; RRID: AB_10001695 |
| Rabbit polyclonal anti-RPA32/RPA2 (pS4, S8) | Novus Biologicals | Cat# NBP1-23017; RRID: AB_1726226 |
| Rat monoclonal anti-RPA32/RPA2 (4E4) | Cell Signaling Technology | Cat# 2208; RRID: AB_2238543 |
| Mouse monoclonal anti-FLAG (M2) | Sigma-Aldrich | Cat# F1804; RRID: AB_262044 |
| Mouse monoclonal anti-α-Tubulin | Sigma-Aldrich | Cat# T-5168; RRID: AB_477579 |
| Rabbit polyclonal anti-RAD51 | Abcam | Cat# ab176458; RRID: AB_2665405 |
| Rabbit polyclonal anti-RIF1 | Gift from Davide Robbiani | N/A |
| Mouse monoclonal anti-GFP | Roche Applied Science | Cat# 11814460001; RRID: AB_390913 |
| IRDye 680RD Goat anti-Mouse IgG (H+L) | LI-COR Biosciences | Cat# 925-68070; RRID: AB_2651128 |
| IRDye 800CW Goat anti-Mouse IgG (H+L) | LI-COR Biosciences | Cat# 926-32210; RRID: AB_621842 |
| IRDye 680RD Goat anti-Rabbit IgG (H+L) | LI-COR Biosciences | Cat# 925-68071; RRID: AB_2721181 |
| IRDye 800CW Goat anti-Rabbit IgG (H+L) | LI-COR Biosciences | Cat# 925-32211; RRID: AB_2651127 |
| Alexa Fluor 488 Goat anti-Mouse IgG (H+L) | Thermo Fisher Scientific | Cat# A11001; RRID: AB_2534069 |
| Alexa Fluor 568 Goat anti-Mouse IgG (H+L) | Thermo Fisher Scientific | Cat# A11031; RRID: AB_144696 |
| Alexa Fluor 568 Goat anti-Rat IgG (H+L) | Thermo Fisher Scientific | Cat# A11077; RRID: AB_2534121 |
| Alexa Fluor 488 Chicken anti-Rabbit IgG (H+L) | Thermo Fisher Scientific | Cat# A21441; RRID: AB_10563745 |
| Alexa Fluor 568 Goat anti-Rabbit IgG (H+L) | Thermo Fisher Scientific | Cat# A11011; RRID: AB_143157 |
| Purified Rat anti-Mouse CD180 (RP/14) | BD Biosciences | Cat# 552128; RRID: AB_394343 |
| Purified Rat anti-Mouse CD16/CD32 (2.4G2) Fc Block™ | BD Biosciences | Cat# 553141; RRID: AB_394656 |
| Biotin Rat anti-Mouse IgG1 (A85-1) | BD Biosciences | Cat# 553441; RRID: AB_394861 |
| PE Rat anti-Mouse B220 (RA3-6B2) | BD Biosciences | Cat# 553088; RRID: AB_10893353 |
| Purified Rat anti-Mouse CD180 (RP/14) | BD Biosciences | Cat# 552128; RRID: AB_394343 |
| IgM Monoclonal Antibody (II/41), FITC | Thermo Fisher Scientific | Cat# 11-5790-81; RRID: AB_465244 |
| Goat anti-Mouse IgA-PE | Southern Biotech | Cat# 1040-09; RRID: AB_2794375 |
| Bacterial and Virus Strains | ||
| Bacteria: TOP10 Chemically Competent E. coli | Thermo Fisher Scientific | Cat# C404006 |
| Bacteria: STBL3 Chemically Competent E. coli | Thermo Fisher Scientific | Cat# C737303 |
| Lentivirus: pRSV-Rev | (Dull et al., 1998) | Cat# 12253; RRID: Addgene_12253 |
| Lentivirus: pMDLg/pRRE | (Dull et al., 1998) | Cat# 12251; RRID: Addgene_12251 |
| Lentivirus: pHCMVG | ATCC | Cat# 75497 |
| Lentivirus: lentiCas9-Blast | (Sanjana et al., 2014) | Cat# 52962; RRID: Addgene_52962 |
| Lentivirus: lentiCRISPRv2 | (Sanjana et al., 2014) | Cat# 52961; RRID: Addgene_52961 |
| Lentivirus: lentiCRISPRv2 neo | (Stringer et al., 2019) | Cat# 98292; RRID: Addgene_98292 |
| Lentivirus: pCW-eGFP-SHLD3 | (Noordermeer et al., 2018) | Cat# 114126; RRID: Addgene_114126 |
| Lentivirus: pLentiGuide-puro GFP-NLS | Gift from Daniel Durocher | N/A |
| Lentivirus: pLentiGuide-puro mCherry-NLS | Gift from Daniel Durocher | N/A |
| Mammalian expression: SP-Cas9 | (D’Astolfo et al., 2015) | Cat# 62731; RRID: Addgene_62731 |
| Mammalian expression: pX330-U6-Chimeric_BB-CBh-hSpCas9 | (Cong et al., 2013) | Cat# 42230; RRID: Addgene_42230 |
| Mammalian expression: pcDNA3.1-Hygro-delta-hCD4 | Gift from Eugene Oltz | N/A |
| Mammalian expression: PB-TRE-dCas9-VPR | (Chavez et al., 2015) | Cat# 63800; RRID: Addgene_63800 |
| Mammalian expression: PB-TRE-mTHAP1 | This paper | N/A |
| Mammalian expression: PB-TRE-mSHLD1 | This paper | N/A |
| Mammalian expression: PB-TRE- mTHAP1C54Y | This paper | N/A |
| Lentivirus: pCVL.SFFV.d14GFP.EF1a.HA.NLS.Sce(opt).T2A.TagBFP | Gift from Andrew Scharenberg | Cat# 32627; RRID: Addgene_32627 |
| Lentivirus: pCVL Traffic Light Reporter 1.1 (Sce target) Ef1a Puro | (Certo et al., 2011) | Cat# 31482; RRID: Addgene_31482 |
| Mammalian expression: pCMV-SV40T | Gift from Kai Ge | N/A |
| Mouse CRISPR Knockout Pooled Library (Brie) | (Doench et al., 2016) | Cat# 73632; RRID: Addgene_73632 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Olaparib | Selleckchem | Cat# AZD2281 |
| Cisplatin | Sigma-Aldrich | Cat# 479306 |
| Lipopolysaccharide (LPS) from E. coli O111:B4 | Sigma-Aldrich | Cat# L2630 |
| Interleukin 4 (IL-4) from mouse | Sigma-Aldrich | Cat# I1020 |
| CD43 microbeads (Ly-48) | Miltenyi Biotec | Cat# 130-049-801 |
| X-tremeGENE™ 9 DNA Transfection Reagent | Roche Diagnostics | Cat# 6365809001 |
| Gibson Assembly Cloning Kit | NEB | Cat# E5510S |
| Zero Blunt™ PCR Cloning Kit | Thermo Fisher Scientific | Cat# K270020 |
| PNA probe for telomeres Cy3-(CCCTAA)3 | PNA Bio | Cat# F1002 |
| DAPI | Thermo Fisher Scientific | Cat# 62248 |
| EdU | Thermo Fisher Scientific | Cat# A10044 |
| Colcemid | Roche Diagnostics | Cat# 10295892001 |
| Dynabeads Protein A | Thermo Fisher Scientific | Cat# 10002D |
| cOmplete, Mini Protease inhibitor cocktail | Roche Diagnostics | Cat# 11836153001 |
| Puregene Proteinase K enzyme | Qiagen | Cat# 158920 |
| Puregene RNase A Solution | Qiagen | Cat# 158924 |
| T4 DNA Polymerase | NEB | Cat# M0203L |
| T4 Polynucleotide Kinase | NEB | Cat# M0201L |
| DNA Polymerase I, Large (Klenow) Fragment | NEB | Cat# M0210L |
| Exonuclease T (ExoT) | NEB | Cat# M0265L |
| Klenow Fragment (3′→5′ exo-) | NEB | Cat# M0212L |
| Quick Ligation Kit | NEB | Cat# M2200L |
| KAPA HiFi HotStart ReadyMix (2X) | KAPA Biosystems | Cat# KK2600 |
| MyOne Streptavidin C1 Beads | ThermoFisher | Cat# 650-01 |
| Agencourt AMPure XP beads | Beckman Coulter | Cat# A63881 |
| Phusion High-Fidelity PCR Master Mix with HF buffer | NEB | Cat# M0531L |
| Recombinant Human TGF-beta 1 Protein | R&D | Cat# 240-B |
| Recombinant Murine sCD40 Lignad | PeproTech | Cat# 315-15 |
| TRIzol | Thermo Fisher Scientific | Cat# 15596018 |
| MyTaq™ Red Mix | Bioline | Cat# BIO-25044 |
| Critical Commercial Assays | ||
| KAPA Library Quantification Kit | Kapa Biosciences | Cat# KK4824 |
| EasySep Human CD4 Positive Selection Kit II | STEMCELL technologies | Cat# 18052 |
| Click-IT EdU Alexa Fluor 488 Flow Cytometry Assay Kit | Thermo Fisher Scientific | Cat# C10425 |
| Click-IT EdU Alexa Fluor 647 Flow Cytometry Assay Kit | Thermo Fisher Scientific | Cat# C10634 |
| Geneticin™ Selective Antibiotic (G418 Sulfate) | Thermo Fisher Scientific | Cat# 10131027 |
| CellTiter-Glo® Luminescent Cell Viability Assay | Promega | Cat# G7571 |
| ESGRO® Recombinant Mouse LIF Protein | Sigma-Aldrich | Cat# ESG1107 |
| Fetal Bovine Serum, embryonic stem cell-qualified | Thermo Fisher Scientific | Cat# 16141079 |
| iSCRIPT Advanced cDNA Synthesis Kit | Bio-Rad | Cat# 1725037 |
| SsoAdvanced™ Universal SYBR Green Supermix | Bio-Rad | Cat# 1725271 |
| Mouse Embryonic Fibroblast Nucleofector™ Kit 2 | Lonza | Cat# VVPD-1005 |
| PrimePCR™ SYBR Green Assay: Actb, Mouse | Bio-Rad | Cat# qMmuCED0027505 |
| PrimePCR™ SYBR Green Assay: 1110034G24Rik, Mouse | Bio-Rad | Cat# qMmuCID0014233 |
| Blood & Cell Culture DNA Midi Kit | QIAGEN | Cat# 13343 |
| ChIP DNA Clean & Concentrator | Zymo Research | Cat# D5205 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GSE154729 |
| RNA-seq and ChIP-seq datasets for Thap1−/− in mESC | (Aguilo et al., 2017) | GSE86911 |
| RNA-seq and ChIP-seq datasets for Yy1flox/flox TAT-Cre in primary B cells | (Nandi et al., 2020a) | GSE145161 |
| ChIP-seq dataset for YY1 in mESC | (Sigova et al., 2015) | GSE68195 |
| ChIP-seq dataset for HCF1 in mESC | (Mouse et al., 2012) | GSE36030 |
| ChIP-seq dataset for THAP1 in K562 cells | (Gertz et al., 2013) | GSE32465 |
| ChIP-seq dataset for HCF1 and YY1 in K562 cells | (Consortium, 2012) | GSE31477 |
| Unprocessed images | This paper | http://dx.doi.org/10.17632/35jfgtzkk4.1 |
| Experimental Models: Cell Lines | ||
| MEF: Wildtype | (Callen et al., 2020) | N/A |
| MEF: Brca1 Δ11/Δ11 | (Callen et al., 2020) | N/A |
| MEF: Thap1−/−Brca1 Δ11/Δ11 Clone 1 | This paper | N/A |
| MEF: Thap1−/−Brca1 Δ11/Δ11 Clone 2 | This paper | N/A |
| MEF: Thap1−/−Brca1 Δ11/Δ11 inducible THAP1 | This paper | N/A |
| MEF: Thap1−/−Brca1 Δ11/Δ11 inducible THAP1C54Y | This paper | N/A |
| MEF: Thap1−/−Brca1 Δ11/Δ11 inducible SHLD1 | This paper | N/A |
| MEF: Wildtype inducible THAP1 | This paper | N/A |
| MEF: Wildtype inducible SHLD1 | This paper | N/A |
| MEF: Shld1−/− inducible THAP1 | This paper | N/A |
| hTERT-RPE1: BRCA1−/− p53−/− | This paper | N/A |
| hTERT-RPE1: THAP1−/−BRCA1−/− p53−/− clone 1 | This paper | N/A |
| hTERT-RPE1: THAP1−/−BRCA1−/− p53−/− clone 2 | This paper | N/A |
| mES: Brca2Y3308X | (Kuznetsov et al., 2008) | N/A |
| mES: Thap1−/−Brca2Y3308X | This paper | N/A |
| Mouse B cell: CH12-F3 | (Nakamura et al., 1996) | N/A |
| Mouse B cell: CH12-F3 Trp53bp1−/− | (Gupta et al., 2018) | N/A |
| Mouse B cell: CH12-F3 Shld1−/− | (Gupta et al., 2018) | N/A |
| Mouse B cell: CH12-F3 Shld3−/− | (Gupta et al., 2018) | N/A |
| Mouse B cell: CH12-F3 Thap1−/− #4 | This paper | N/A |
| Mouse B cell: CH12-F3 Thap1−/− #12 | This paper | N/A |
| Experimental Models: Organisms/Strains | ||
| Mouse: BRCA1+/Δ11. B6/129 | NCI mouse repository | Strain # 01XC9 |
| Mouse: BRCA1FΔ11/FΔ11CD19Cre. B6/129 | NCI mouse repository | Strain # 01XC8 |
| Mouse: 53BP1−/−. B6/129 | (Ward et al., 2003) | N/A |
| Mouse: SHLD1−/−. B6/129 | This paper | N/A |
| Oligonucleotides | ||
| sgRNA to generate mouse Thap1−/− cells, see Table S3 | This paper | N/A |
| sgRNA to generate mouse Shld1−/− cells, see Table S3 | This paper | N/A |
| sgRNA to generate human THAP1−/− cells, see Table S3 | This paper | N/A |
| Primers used for sgRNA target site mutation in mouse Thap1, see Table S3 | This paper | N/A |
| Primers used for generation of THAP1C54Y mutation, see Table S3 | This paper | N/A |
| sgRNA to generate THABS−/− cells, see Table S3 | This paper | N/A |
| sgRNA used for generation of Shld1−/− mouse, see Table S3 | This paper | N/A |
| Primers used for genotyping of Shld1−/− mouse, see Table S3 | This paper | N/A |
| Primers used for PCR of sgRNA for illumina sequencing, see Table S3 | (Doench et al., 2016) | N/A |
| Software and Algorithms | ||
| ZEN 2 (blue edition) | Zeiss | https://www.zeiss.com/ |
| Metafer 4 | MetaSystems | https://metasystems-international.com/ |
| Prism 8 | GraphPad | https://www.graphpad.com/ |
| ImageJ | National Institutes of Health | https://imagej.nih.gov/ij |
| RStudio | RStudio Team | https://www.rstudio.com/ |
| FlowJo (10.1) | FlowJo LLC | https://www.flowjo.com/ |
| Bowtie 1.1.2 | (Langmead et al., 2009) | https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.2/ |
| MACS 1.4.3 | (Zhang et al., 2008) | https://pypi.org/pypi/MACS/1.4.3 |
| UCSC database | (Karolchik et al., 2004) | https://genome.ucsc.edu |
| UCSC genome browser | (Kent et al., 2002) | https://genome.ucsc.edu |
| Bedtools | (Quinlan and Hall, 2010) | https://github.com/arq5x/bedtools2 |
| R 3.6.1 | R Core Team | https://www.r-project.org/ |
| MAGeCK software package version 0.5.9.2 | (Wang et al., 2019) | https://sourceforge.net/projects/mageck/files/0.5/ |
| Other | ||
| 293T lentivirus packaging cells | ATCC | Cat# CRL-11268; RRID: CVCL_1926 |
| P19 mouse cells | ATCC | Cat# CRL-1825; RRID: CVCL_2153 |
| Glass Bottom Microwell Dishes | MatTek Corporation | Cat# P35G-1.5-14-C |
| Axio Observer Z1 epifluorescence microscope | Zeiss | N/A |
| IN Cell Analyzer | GE Healthcare | N/A |
| Odyssey® CLx Imaging System | LI-COR Biosciences | N/A |
| FACSCalibur | BD Biosciences | N/A |
| Nano Quant Infinite M200 Pro microplate reader | Tecan | N/A |
| Mark 1 137Cs irradiator | JL Shepherd | N/A |
| Cytogenetic drying chamber | Thermotron | N/A |
| CFX96 Real-Time System | Bio-Rad | N/A |
| Amaxa Nucleofector IIb | Lonza | N/A |
| FACSAria II cell sorter | BD Biosciences | N/A |
| FACSCanto II | BD Biosciences | N/A |
| Lion heart LX automated microscope | BioTek | N/A |