| Antibodies |
|
|
| Mouse monoclonal anti-alpha Tubulin antibody Clone DM1A |
Abcam |
Cat# ab7291; RRID:AB_2241126 |
| Mouse monoclonal anti-alpha-Tubulin antibody |
Sigma-Aldrich |
Cat# T5168; RRID:AB_477579 |
| PE mouse monoclonal anti-Human CD54 antibody Clone HA58 |
BD Biosciences |
Cat# 555511; RRID:AB_395901 |
| FITC Mouse monoclonal Anti-Human CD40 antibody Clone 5C3 |
BD Biosciences |
Cat# 555588; RRID:AB_395963 |
| Rabbit polyclonal anti-FBXO11 antibody |
Bethyl Laboratories |
Cat# A301–177A-T; RRID:AB_2779727 |
| Rabbit polyclonal anti-CTBP1 antibody |
Bethyl Laboratories |
Cat# A300–338A-T; RRID:AB_2779159 |
| Rabbit polyclonal anti-CtBP antibody |
Santa Cruz Biotechnology |
Cat# sc-11390; RRID:AB_2086634 |
| Rabbit monoclonal anti-DUSP10 antibody Clone EPR9366 |
Abcam |
Cat# ab140123 |
| Mouse monoclonal anti-CD40 antibody Clone H10 |
Santa Cruz Biotechnology |
Cat# sc-13128; RRID:AB_627060 |
| Anti-rabbit IgG, HRP-linked Antibody |
Cell Signaling Technology |
Cat# 7074; RRID:AB_2099233 |
| Anti-mouse IgG, HRP-linked Antibody |
Cell Signaling Technology |
Cat# 7076; RRID:AB_330924 |
| Influenza hemagglutinin (HA) epitope (YPYDVPDYA) antibody |
Covance Research Products Inc |
Cat# MMS-101P; RRID:AB_2314672 |
| Rabbit polyclonal anti-TBP Antibody |
Bethyl Laboratories |
Cat# A301–229A-T; RRID:AB_890661 |
| APC Mouse monoclonal anti-human CD95 (Fas) Antibody Clone DX2 |
Biolegend |
Cat# 305612; RRID:AB_2782770 |
| Mouse monoclonal anti-GAPDH antibody |
Abcam |
Cat# ab8245; RRID:AB_2107448 |
| FITC Mouse monoclonal anti-human CD21 antibody Clone Bu32 |
Biolegend |
Cat# 354909; RRID:AB_2561574 |
| FITC Mouse monoclonal anti-human CD37 antibody Clone M-B371 |
Biolegend |
Cat# 356304; RRID:AB_2561837 |
| Mouse monoclonal Anti-NF-kappaB p52 antibody |
Millipore |
Cat# 05–361; RRID:CVCL_8H75 |
| Mouse monoclonal anti-Human CD19 Alexa Fluor 488 antibody |
eBioscience |
Cat# 53–0199–41; RRID:AB_1659679 |
| Rabbit polyclonal anti-NF-kappaB2 p100/p52 antibody |
Cell Signaling Technology |
Cat# 4882S; RRID:AB_10695537 |
| Rabbit monoclonal anti-ZIP7/SLC39A7 antibody Clone D103A |
Cell Signaling Technology |
Cat# 33176S; RRID:AB_2799032 |
| Rabbit monoclonal anti-phospho-p44/42 MAPK (Erk 1/2) (Thr202/Tyr204) Clone D13.14.4E |
Cell Signaling Technology |
Cat# 4370s; RRID:AB_2315112 |
| Rabbit polyclonal anti-p44/42 MAPK (Erk 1/2) antibody |
Cell Signaling Technology |
Cat# 9102S; RRID:AB_330744 |
| Rabbit monoclonal anti-phospho-p38 MAPK (Thr80/Tyr182) antibody Clone D3F9 |
Cell Signaling Technology |
Cat# 4511S; RRID:AB_2139682 |
| Rabbit monoclonal anti-p38 antibody Clone D13E1 |
Cell Signaling Technology |
Cat# 8690s; RRID:AB_10999090 |
| Rabbit polyclonal anti-phospho-SAPK/JNK (Thr183/Tyr185) antibody |
Cell Signaling Technology |
Cat# 9251s; RRID:AB_331659 |
| Rabbit polyclonal anti-SAPK/JNK antibody |
Cell Signaling Technology |
Cat# 9252s; RRID:AB_2250373 |
| Rabbit polyclonal anti-METTL14 antibody |
Novus Biologicals |
Cat# NBP1–81392; RRID:AB_11021780 |
| Mouse monoclonal anti-CUG-BP1 antibody Clone 3B1 |
Santa Cruz Biotechnology |
Cat# sc-20003; RRID:AB_627319 |
| Rabbit polyclonal V5 antibody |
Bethyl |
Cat# A190–120P; RRID:AB_162729 |
| Rabbit monoclonal anti-BCL6 antibody Clone D4I2V |
Cell Signaling Technology |
Cat# 14895; RRID:AB_2798638 |
| Rabbit monoclonal anti-TRAF5 antibody Clone D3E2R |
Cell Signaling Technology |
Cat# 41658; RRID:AB_2799205 |
| Mouse monoclonal anti-VPS25 antibody Clone B-4 |
Santa Cruz Biotechnology |
Cat# sc-271648; RRID:AB_10707989 |
| Mouse monoclonal anti-CHAMP5 antibody Clone F-7 |
Santa Cruz Biotechnology |
Cat# sc-374338; RRID:AB_10989738 |
| Peroxidase IgG Fraction Monoclonal mouse antiRabbit IgG, light chain specific |
Jackson ImmunoResearch |
Cat# 211–032–171; RRID:AB_2339149 |
| APC Mouse monoclonal anti-mouse CD95 (Fas) antibody Clone SA367H8 |
Biolegend |
Cat# 152604; RRID:AB_2632899 |
| FITC Rat monoclonal anti-mouse CD19 antibody Clone 1D3/CD19 |
Biolegend |
Cat# 152403; RRID:AB_152403 |
| APC Rat monoclonal anti-mouse CD40 antibody Clone 3/23 |
Biolegend |
Cat# 124612; RRID:AB_1134072 |
| PE Rat monoclonal anti-mouse IgG1 antibody Clone A85–1 |
BD Biosciences |
Cat# 550083; RRID:AB_393553 |
| APC Rat monoclonal anti-mouse CD45R/B220 antibody Clone RA3–6B2 |
BD Biosciences |
Cat# 561880; RRID:AB_10897020 |
| Armenian hamster monoclonal anti-Mouse/Rat CD40 antibody Clone HM40–3 |
eBioscience |
Cat# 14–0402–81; RRID:AB_467227 |
| Mouse Ubiquitin (P4D1) monoclonal antibody |
Cell Signaling Technology |
Cat# 3936S; RRID:AB_331292 |
| Rabbit kBa polyclonal antibody |
Cell Signaling Technology |
Cat# 9242S; RRID:AB_331623 |
| Rabbit monoclonal CD40 antibody |
Abcam |
Cat# ab224639 |
| Mouse monoclonal LAMP1 antibody |
Cell Signaling Technology |
Cat# 15665; RRID:AB_2798750 |
| Alexa Fluor 488-AffiniPure Goat Anti-Mouse IgG (H+L) |
FISHER SCIENTIFIC |
Cat# NC0260529; RRID:AB_2338840 |
| Alexa Fluor 594-AffiniPure Goat Anti-Rabbit IgG (H+L) |
FISHER SCIENTIFIC |
Cat# NC0414256; RRID:AB_2338059 |
| Rabbit polyclonal Virilizer (VIRMA) Antibody |
Bethyl Laboratories |
Cat# A302–124A; RRID:AB_1720422 |
| Bacterial and Virus Strains |
|
|
| B95.8 Epstein-Barr Virus |
Dr. Elliott Kieff |
N/A |
| Chemicals, Peptides, and Recombinant Proteins |
|
|
| Dynabeads® Protein G |
Thermo Scientific |
Cat# 10003D |
| Agencourt AMPure XP SPRI beads |
Beckman Coulter |
Cat# A63880 |
| MEGA CD40L |
Enzo life sciences |
Cat# ALX-522- 110-C010 |
| CD40L (human) (multimeric) |
Adipogen Life Sciences |
Cat# AG-40B- 0010-C010 |
| Bortezomib |
Apex bio |
Cat# A2614 |
| polybrene |
Sigma-Aldrich |
Cat# TR-1003-G |
| Recombinant Human TNF-alpha Protein |
R&D systems |
Cat# 210-TA-005 |
| IKK-2 inhibitor VIII |
Calbiochem |
Cat# 401487 |
| Recombinant Murine IL-4 |
PeproTech |
Cat# 214–14 |
| InSolution Leupeptin |
MilliporeSigma |
Cat# 509281 |
| Cathepsin Inhibitor I |
MilliporeSigma |
Cat# 219415 |
| Hoechst |
Molecular Probes |
Cat# 33258 |
| 16% formaldehyde |
Ted Pella Inc. |
Cat# 9658705 |
| E-64 Protease Inhibitor |
MilliporeSigma |
Cat# 324890 |
| Normal goat serum |
Invitrogen |
Cat# 31873 |
| Cyclonheximide solution |
MilliporeSigma |
Cat# 66–81–9 |
| InSolution Pepstatin A |
MilliporeSigma |
Cat# 508437 |
| Critical Commercial Assays |
|
|
| RNeasy Mini Kit |
QIAGEN |
Cat# 74104 |
| miRNeasy Mini Kit |
QIAGEN |
Cat# 217004 |
| Power SYBR Green RNA-to-Ct 1-Step Kit |
Applied Biosystems |
Cat# 4389986 |
| QiAquick PCR Purification Kit |
QIAGEN |
Cat# 28106 |
| QIAquick Gel Extraction Kit |
QIAGEN |
Cat# 28704 |
| RNase-Free DNase Set |
QIAGEN |
Cat# 79254 |
| iScript Reverse Transcription Supermix for RT- qPCR |
BIO-RAD |
Cat# 1708841 |
| Power SYBR Green PCR Master Mix |
Applied Biosystems |
Cat# 4367659 |
| Gateway LR Clonase II Enzyme Mix |
Invitrogen |
Cat# 11789–020 |
| QIAprep Spin Miniprep Kit |
QIAGEN |
Cat# 27106 |
| Invitrogen PureLink Quick Plasmid Maxiprep Kit |
Invitrogen |
Cat# K210016 |
| Dead Cell Removal Kit |
Miltenyi Biotec |
Cat# 130–090–101 |
| NEBNext Poly(A) mRNA Magnetic Isolation Module |
New England Biolabs |
Cat# E7490 |
| NEBNext Ultra RNA Library Prep Kit for Illumina |
New England Biolabs |
Cat# E7530 |
| RosetteSep Human B Cell Enrichment Cocktail; Immunodensity isolation of untouched B cells |
StemCell Technologies, Inc. |
Cat# 15064 |
| EasySep Human B cell enrichment kit |
StemCell Technologies, Inc. |
Cat# 19054 |
| MycoAlert Mycoplasma Detection Kit |
Lonza |
Cat# LT07–218 |
| Blood and Cell Culture DNA Maxi Kit |
QIAGEN |
Cat# 13362 |
| DNeasy Blood& Tissue Kit |
QIAGEN |
Cat# 69504 |
| Magna RIP RNA-Binding Protein Immunoprecipitation Kit |
MilliporeSigma |
Cat# 17–700 |
| CD40 Gene expression Assays (Hs00386848_m1) |
Thermo Fisher Scientific |
Cat# 4448892 |
| TaqMan Fast Virus 1-Step Master Mix |
TaqMan Fast Virus 1-Step Master Mix |
Cat# 4444432 |
| Deposited Data |
|
|
| Resting and CD40L-stimulated primary B cell RNA-seq datasets Deposited into the NIH GEO omnibusRaw and analyzed data |
Gewurz Laboratory |
GSE101666 |
| Experimental Models: Cell Lines |
|
|
| GM12878 lymphoblastoid cell line (LCL) |
Coriell Institute for Medical Research |
N/A |
| EBV+ Burkitt lymphoma Daudi cell line |
ATCC |
CCL-213 |
| EBV- Burkitt lymphoma Akata cell line |
Dr. Bo Zhao |
N/A |
| P3HR1 clone 16 |
Dr. Elliott Kieff |
N/A |
| Burkitt lymphoma KEM I cell line |
Dr. Jeff Sample |
N/A |
| Burkitt lymphoma BJAB cell line |
Dr. Bo Zhao |
N/A |
| Burkitt lymphoma MUTU I cell line |
Dr. Jeff Sample |
N/A |
| GM12878-Cas9 |
This paper |
N/A |
| P3HR1-Cas9 |
This paper |
N/A |
| BJAB-Cas9 |
This paper |
N/A |
| MutuI-Cas9 |
This paper |
N/A |
| KemI-Cas9 |
This paper |
N/A |
| Akata-Cas9 |
This paper |
N/A |
| Daudi-Cas9 |
This paper |
N/A |
| HEK293T |
ATCC |
CRL-3216 |
| Experimental Models: Organisms/Strains |
|
|
| FBX011 f/f/C D19Cre+ mice |
Dr. Roberto Chiarle |
N/A |
| FBXO11f/f/CD19WT mice |
Dr. Roberto Chiarle |
N/A |
| Oligonucleotides |
|
|
| Table S3 |
This paper |
N/A |
| Table S4 |
This paper |
N/A |
| Recombinant DNA |
|
|
| pLX-TRC313 CELF1 (rescue cDNA) |
This paper |
N/A |
| pLX-TRC313 |
Broad Institute |
N/A |
| pLentiGuide-Puro |
Addgene |
Cat# 52963 |
| pLenti SpBsmBI sgRNA Hygro |
Addgene |
Cat# 62205 |
| pLentiCas9-Blast |
Addgene |
Cat# 52962 |
| pXPR-011 |
John Doench |
N/A |
| Avana CRISPR Lentivirus Library |
Broad Institute |
N/A |
| pGL3-p27Luc |
Addgene |
Cat# 23047 |
| pIS2 |
Addgene |
Cat# 12177 |
| CD40 (Homo sapiens) in pENTR223 |
DNASU |
Cat# HsCD00508711 |
| BCL6 (Homo sapiens) in pENTR223 |
DNASU |
Cat# HsCD00516212 |
| Software and Algorithms |
|
|
| STARS v1.2 |
Doench et al., 2016 |
http://portals.broadinstitute.org/gpp/public/software/stars |
| STAR2.5.2b |
Dobin et al., 2013 |
https://github.com/alexdobin/STAR |
| FlowJo_V10 |
FLOWJO LLC |
https://www.flowjo.com/ |
| DESeq2 v1.14.1 |
Love et al., 2014 |
https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| GraphPad Prism 7 |
GraphPad Software |
https://www.graphpad.com/scientific-software/prism/ |
| SRAMP: A sequence-based N6-methyladenosine (m6A) modification site predictor |
Zhou et al., 2016 |
http://www.cuilab.cn/sramp/ |
