KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-CTCF, rabbit polyclonal | Millipore | Cat# 107-729; RRID: AB_441965 |
| Anti-Rad21, rabbit polyclonal | Abcam | Cat# ab992; RRID: AB_2176601 |
| Topo IIβ, rabbit polyclonal | Santa Cruz | Cat# sc13059, clone H-286: RRID: AB_2205866 |
| RP105 (Purified Rat Anti-Mouse CD180) | BD Biosciences | Cat# 552128; RRID: AB_394343 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Etoposide | Sigma Aldrich | Cat# E1383 |
| Trizol | Invitrogen | Cat# 15596026 |
| 5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) | Sigma Aldrich | Cat# D1916 |
| Mouse IFN Beta | PBL Assay Science | Cat# 12405-1 |
| Imatinib mesylate (STI-571) | Selleckchem | Cat# S1026 |
| Lipopolysaccharide (LPS) | Sigma Aldrich | Cat# L-2630 |
| Doxycycline hyclate | Sigma Aldrich | Cat# D9891 |
| 4-Hydroxytamoxifen | Sigma Aldrich | Cat# H7904 |
| IL-4 from mouse, Interleukin-4, recombinant | Sigma Aldrich | Cat# I-1020 |
| Lovastatin | Abcam | Cat# ab120614 |
| 3-indole acetic acid | Sigma Aldrich | Cat# I3750 |
| Recombinant TDP2 | Gao et al., 2012 | N/A |
| Epoxomicin | Sigma Aldrich | Cat# E3652 |
| 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 |
| Exonuclease VII (ExoVII) | NEB | Cat# M0379L |
| Klenow Fragment (3′→5′ exo-) | NEB | Cat# M0212L |
| Quick Ligation Kit | NEB | Cat# M2200L |
| USER enzyme | NEB | Cat# M5505L |
| 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 |
| TDP2 substrate (Cy5-5′Tyrosine-ssDNA19-BHQ) | Zagnoli-Vieira et al., 2018 | N/A |
| TDP1 substrate (BHQ-ssDNA13-3′Tyrosine-Cy5) | Zagnoli-Vieira et al., 2018 | N/A |
| Critical Commercial Assays | ||
| Click-IT EdU Alexa Fluor 488 Flow Cytometry Assay Kit | ThermoFisher | Cat# C10425 |
| Click-iT RNA Alexa Fluor 594 Imaging kit | ThermoFisher | Cat# C10330 |
| Anti-CD43 (Ly-48) MicroBeads mouse | Miltenyi Biotech | Cat# 130-049-80 |
| NEBNext rRNA Depletion kit | NEB | Cat# E6310S |
| Click-iT Nascent RNA Capture Kit | ThermoFisher | Cat# C10365 |
| KAPA Library Quantification Kit | Kapa Biosciences | Cat# KK4824 |
| CHEF Mammalian Genomic DNA plug kit | Bio-Rad | Cat# 1703591 |
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
| Deposited Data | ||
| Raw and analyzed data | This paper | GSE129529 |
| ChIP-seq CTCF MEF B6 | Canela et al., 2017 | GSM2635593 |
| AsiSI and RAG preB exoT and exoT exoVII | Canela et al., 2016 | PRJNA326246 |
| Scans of the radioactive gels for the ExoVII and ExoT in vitro blunting assay | This paper | https://doi.org/10.17632/2gsyvtr9c4.1 |
| Experimental Models: Cell Lines | ||
| Pre-B cell lines | Bredemeyer et al., 2006 | N/A |
| HCT116 cell lines (gift from Masato Kanemaki) | Natsume et al., 2016 | N/A |
| Primary MEFs WT, Smc3−/F, WaplF/F | Busslinger et al., 2017 | N/A |
| Pre-B cell line Lig4−/−, tet-inducible ZFN, tet-inducible AsiSI | Canela et al., 2016 | N/A |
| Pre-B cells Tdp2−/− and Lig4−/− Tdp2−/− | This paper | N/A |
| Experimental Models: Organisms/Strains | ||
| C57BL/6NCr mice | Charles River | Strain code# 027 |
| Top2β−/− mice | Yang et al., 2000 | N/A |
| Oligonucleotides | ||
| END-seq adaptor 1, 5′-phosphate-GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUU[Biotin-dT]U[Biotin-dT]UUACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′ | Canela et al., 2016 | N/A |
| END-seq adaptor 2, 5′-phosphate-GATCGGAAGAGCACACGTCUUUUUUUUAGACGTGTGCTCTTCCGATC*T-3′ | Canela et al., 2016 | N/A |
| TruSeq barcoded primer p5, 5′-AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ (N = barcode) | This paper | N/A |
| TruSeq barcoded primer p7, 5′-CAAGCAGAAGACGGCATACGAGANNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T -3′ (N = barcode) | This paper | N/A |
| Illumina truncated adaptor 1, 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ | Canela et al., 2017 | N/A |
| Illumina truncated adaptor 2, 5′-phosphate-GATCGGAAGAGCACACGTCT-3′ | Canela et al., 2017 | N/A |
| YT18, 5′-tyrosine-TCCGTTGAAGCCTGCTTT-3′ | Gao et al., 2012 | N/A |
| T22 5′-GCGCAGCTAGCGGCGGATG*G*C*A-3′ | This paper (modified from Gao et al., 2012) | N/A |
| B36 5′-phosphate-TGCCATCCGCCGCTAGCTGCGCAAAGCAGGCTTCAA-3′ | Gao et al., 2012 | N/A |
| B40 5′-phosphate-TGCCATCCGCCGCTAGCTGCGCAAAGCAGGCTTCAACGGA-3′ | Gao et al., 2012 | N/A |
| ZNF-bio 5′-/Biosg/CAGAAGCCTTCAGTATGCACCA-3′ | This paper | N/A |
| I7-ZNF-nested-barcode 5′-CTCGGCATTCCTGCTGAACCGCTCTTCCGATCTNNNNNNNNTTCCACTTAACCCCAACTCCAG-3′ (N = barcode) |
This paper (modified from Hu et al., 2016) | N/A |
| Adaptor-upper 5′-GGTACACGACGCTCTTCCGATCTNNNNNN/3AmMO/-3′ | This paper (modified from Hu et al., 2016) | N/A |
| Adaptor-lower 5′-phosphate-AGATCGGAAGAGCGTCGTGTACC/3AmMO/-3′ | This paper (modified from Hu et al., 2016) | N/A |
| I5-bridge 5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ | This paper (modified from Hu et al., 2016) | N/A |
| P5-I5c 5′-AATGATACGGCGACCACCGAGATCTACACTCTTT*C-3′ | This paper (modified from Huetal., 2016) | N/A |
| P7-I7c 5′-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTT*C-3′ | Hu et al., 2016 | N/A |
| Software and Algorithms | ||
| 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 3.3.1 | R Core Team, 2008 | https://www.r-project.org/ |