REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rat anti-CD40 Clone 1C10	BioLegend	Cat# 102810; RRID: AB_629065
Rat anti-CD180 (RP/14)	BD Biosciences	Cat# 552128; RRID: AB_394343
Mouse anti-Flag M2	Sigma-Aldrich	Cat# F3165; RRID: AB_259529
Mouse anti-Flag M2 (HRP conjugated)	Sigma-Aldrich	Cat# A8592; RRID: AB_439702
Rabbit anti-Rif1	Di Virgilio et al., 2013	N/A
Rabbit anti-ZMYND8	Sigma-Aldrich	Cat# HPA020949; RRID: AB_1857223
Mouse anti-γH2AX (Ser139) Clone JBW301	Millipore/Merck	Cat# 05-636; RRID: AB_309864
Mouse anti-β Actin Clone AC-15	Sigma-Aldrich	Cat# A5441; RRID: AB_476744
Mouse anti-53BP1	Bethyl	Cat# A300-272A; RRID: AB_185520
Mouse anti-53BP1 Clone BP18	Millipore/Merck	Cat# 05-725; RRID: AB_309939
Mouse anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) Clone 4H8	Abcam	Cat# ab5408; RRID: AB_304868
Rat anti-CD21/CD35-FITC Clone 7G6	BD Biosciences	Cat# 561769; RRID: AB_10924591
Rat anti-IgD-FITC Clone 11-26c.2a	BD Biosciences	Cat# 562022; RRID: AB_10894208
Rat anti-IgM-PE Clone R6-60.2	BD Biosciences	Cat# 553409; RRID: AB_394845
Rat anti-IgM-FITC Clone II/41	BD Biosciences	Cat# 553437; RRID: AB_394857
Rat anti-CD43-PE Clone S7	BD Biosciences	Cat# 561857; RRID: AB_10926206
Rat anti-CD23-PE Clone B3B4	BioLegend	Cat# 101607; RRID: AB_312832
Rat anti-CD3-PE Clone 17A2	BioLegend	Cat# 100206; RRID: AB_312663
Rat anti-CD19-APC Clone 6D5	BioLegend	Cat# 115512; RRID: AB_313647
TruStain fcX Rat anti-CD16/32 Clone 93	BioLegend	Cat# 101320; RRID: AB_1574975
Rat anti-B220/CD45R-FITC Clone RA3-6B2	BioLegend	Cat# 103205; RRID: AB_312990
Rat anti-CD38-Alexa700 Clone 90	Invitrogen	Cat# 56-0381-82; RRID: AB_657740
Hamster anti-CD95/Fas-PE Clone Jo2	BD Biosciences	Cat# 561985; RRID: AB_10895586
Rat anti-IgG2b-PE Clone RMG2b-1	BioLegend	Cat# 406707; RRID: AB_2563380
Goat anti-IgA-PE	Southern Biotech	Cat# 1040-09
Rat anti-IgG1-APC Clone X56	BD Biosciences	Cat# 550874; RRID: AB_398470
Rat anti-IgG3-BIOT Clone R40-82	BD Biosciences	Cat# 553401; RRID: AB_394838
Streptavidin-APC	BD Biosciences	Cat# 554067; RRID: AB_10050396
Streptavidin-AP Conjugate	Sigma-Aldrich	Cat# 11089161001
Goat anti-Lamda-UNLB	Southern Biotech	Cat# 1060-01
Goat anti-Kappa-UNLB	Southern Biotech	Cat# 1050-01; RRID: AB_2737431
Mouse IgM-UNLB Clone 11E10	Southern Biotech	Cat# 0101-01; RRID: AB_2629437
Mouse IgG1-UNLB Clone 15H6	Southern Biotech	Cat# 0102-01
Goat anti-IgM, Human ads-BIOT	Southern Biotech	Cat# 1020-08; RRID: AB_2737441
Goat anti-IgG1, Human ads-BIOT	Southern Biotech	Cat# 1070-08
Rat anti-CD43 (Ly-48) Microbeads	Miltenyi Biotec	Cat# 130-049-801
Goat anti-rabbit Alexa546	Invitrogen	Cat# A-11035; RRID: AB_2534093
Goat anti-mouse Alexa488	Invitrogen	Cat# A-11029; RRID: AB_2534088
Anti-BrdU beads	Santa Cruz Biotech	Cat# sc-32323; RRID: AB_626766
Chemicals, Peptides, and Recombinant Proteins
LPS	Sigma-Aldrich	Cat# L2630
IL-4 (mouse recombinant)	Sigma-Aldrich	Cat# I1020
BAFF (human recombinant)	PeproTech	Cat# 310-13
TGFβ-1 (mouse recombinant)	R&D Systems	Cat# 7666-MB-005/CF
Puromycin dihydrochloride	Sigma-Aldrich	Cat# P8833
SILAC-RPMI	Thermo Scientific	Cat# 88421
Dialyzed fetal bovine serum	GIBCO	Cat# 26400-044
13C6 L-arginine	Cambridge Isotope Laboratories	Cat# CLM-2265-H-PK-1
13C6 L-lysine	Cambridge Isotope Laboratories	Cat# CLM-2247-H-PK-1
Non-labeled L-arginine	Sigma-Aldrich	Cat# A8094
Non-labeled L-lysine	Sigma-Aldrich	Cat# L8662
Polyvinylpyrrolidone	Sigma-Aldrich	Cat# PVP40
Complete EDTA-free protease inhibitor cocktail	Roche	Cat# 11873580001
Phosphatase inhibitor cocktail tablets	Roche	Cat# 04906837001
Benzonase	Sigma-Aldrich	Cat# E1014
Glutaraldehyde	Sigma-Aldrich	Cat# 340855
3XFlag peptide	Sigma-Aldrich	Cat# F4799
NuPage LDS Sample buffer	Thermo Fisher Scientific	Cat# NP0008
ATMi KU55933	Tocris Bioscience	Cat# 3544
Carboxyfluorescein succinimidyl ester (CFSE)	Invitrogen	Cat# 65-0850-84
CellTrace Violet	Thermo Fisher Scientific	Cat# C34557
Alum	Sigma-Aldrich	Cat# 31242 (Discontinued)
NP-CGG16	Biosearch Technologies	Cat# N5055B
Paraformaldehyde	Sigma-Aldrich	Cat# P6148
Crystal Violet	Sigma	Cat# C0775
PARPi Olaparib/AZD2281, Ku-0059436	Selleckchem	Cat# S1060
Pierce 16% Formaldehyde Methanol-free	Thermo Scientific	Cat# 28906
TRIzol	Invitrogen	Cat# 15596018
Colcemid	Sigma-Aldrich	Cat# 10295892001
KaryoMAX Giemsa Stain Solution	GIBCO	Cat# 10092013
Gurr Buffer Tablets	GIBCO	Cat# 10582013
Dynabeads Protein A	Invitrogen	Cat# 10001D
Dynabeads M-270 Epoxy	Invitrogen	Cat# 14301
TRIzol LS Reagent	Invitrogen	Cat# 10296028
Critical Commercial Assays
Neon Transfection System, 100 μL Kit	Invitrogen	Cat# MPK10025
APC BrdU Flow Kit	BD Biosciences	Cat# 552598
AllPrep DNA/RNA Mini Kit. Dan	QIAGEN	Cat# 80204
Ribo-Zero Gold rRNA Removal Kit	Illumina	Cat# MRZG12324
TruSeq Stranded Total RNA Library Prep Kit	Illumina	Cat# 20020597
RNeasy Mini Kit	QIAGEN	Cat# 74104
SuperScript VILO cDNA Synthesis Kit	Invitrogen	Cat# 11754250
RapidOut DNA Removal Kit	Thermo Scientific	Cat# K2981
TOPO TA Cloning Kit	Invitrogen	Cat# 450641
Phusion High-Fidelity DNA Polymerase	Thermo Scientific, NEB	Cat# F530L, Cat# M0530L
Luna Universal qPCR Mastermix	NEB	Cat# M3003
NucleoSpin DNA Purification Kit	Macherey-Nagel	Cat# 740499
TURBO DNase	Invitrogen	Cat# AM2239
RNA Fragmentation Reagents	Invitrogen	Cat# AM8740
BioSpin P-30 Gel Columns	Bio-Rad	Cat# 7326232
T4 Polynucleotide Kinase	NEB	Cat# M0201L
Exonuclease I	NEB	Cat# M0293L
ChIP DNA Clean and Concentrator Kit	Zymo Research Corporation	Cat# D5205
RNase H	Thermo Scientific	Cat# 18021071
APE1	NEB	Cat# M0282L
Deposited Data
Raw and analyzed data	This paper	GEO: GSE118794
Original scans and IF images	This paper; Mendeley Data	https://doi.org/10.17632/jktyjvy9hg.1
Experimental Models: Cell Lines
Murine: CH12 (CH12F3) - WT, parental	Nakamura et al., 1996	N/A
Murine: CH12 - WTc, clonal derivative	This paper	N/A
Murine: AID−/− CH12	This paper and Kerafast	Cat# ESP013
Murine: 53bp1−/− CH12	This paper	N/A
Murine: Rif1−/− CH12	This paper	N/A
Murine: Zmynd8-KO1 CH12	This paper	N/A
Murine: Zmynd8-KO2 CH12	This paper	N/A
Murine: Zmynd8-KO3 CH12	This paper	N/A
Murine: iMEFs - WTc, clonal derivative	This paper	N/A
Murine: iMEFs - Rc-1	This paper	N/A
Murine: iMEFs - Rc-2	This paper	N/A
Murine: Zmynd8-KO1 iMEFs	This paper	N/A
Murine: Zmynd8-KO2 iMEFs	This paper	N/A
Murine: Zmynd8-KO3 iMEFs	This paper	N/A
Experimental Models: Organisms/Strains
Mouse: C57BL6: WT	The Jackson Laboratory	JAX# 664
Mouse: Rif1FH/FH	Cornacchia et al., 2012	N/A
Mouse: AID−/−	Muramatsu et al., 2000	N/A
Mouse: Zmynd8tm1a	European Mouse Mutant Archive	EMMA# 05720
Mouse: ROSA26Flpo	The Jackson Laboratory	JAX# 007844
Mouse: Cd19Cre/+	Rickert et al., 1997	N/A
Mouse: Zmynd8F/F	This paper	N/A
Mouse: Zmynd8F/FCd19Cre/+	This paper	N/A
Oligonucleotides
ZMYND8 genotyping primers	See Table S5	N/A
gRNAs for gene editing	See Table S5	N/A
Primers for qPCR	See Table S5	N/A
gRNAs for end resection assay	See Table S5	N/A
Primers for end resection assay	See Table S5	N/A
Primers for Sμ-Sγ1 junctions	See Table S5	N/A
Primers for SHM	See Table S5	N/A
Recombinant DNA
Plasmid: pMX-ZMYND8-3XFlag	This paper	N/A
Plasmid: pX458 (pSpCas9(BB)-2A-GFP (PX458))	Addgene	Cat# 48138
Plasmid: pX458 expressing Cas9D10A	This paper	N/A
Software and Algorithms
MaxQuant (v.1.2.2.5)	Cox and Mann, 2008	N/A
BWA mem	Li and Durbin, 2009	N/A
HOMER ChIP-Seq program	Heinz et al., 2010	N/A
R and ChIPseeker package	Yu et al., 2015	N/A
kallisto v.0.43.0	Bray et al., 2016	N/A
R package tximport	Soneson et al., 2015	N/A
DESeq2	Love et al., 2014	N/A
Bowtie	Langmead et al., 2009	N/A