KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER | |
|---|---|---|---|
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| Antibodies | |||
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| Rabbit polyclonal anti-ZMYND8 | Sigma-Aldrich | Product #HPAG2G949; Lot #A96431; RRID:AB_1B57223 | |
| Rabbit polyclonal anti-BRD4 | Bethyl | Product #A3G1–9B5A1GG; RRID:AB_262G1B4 | |
| Rabbit monoclonal anti-IRF8 | Abcam | Product #ab2G741B, Lot #GR327157B-1 | |
| Rabbit polyclonal anti-ZMYND8 | Bethyl | Product #A3G2-GB9A; RRID:AB_16G42B2 | |
| Monoclonal ANTI-FLAG® M2 antibody | Sigma-Aldrich | Cat# F1BG4; RRID: AB_262G44 | |
| Mouse monoclonal anti-HA (clone 12CA5) | Laboratory of Gerd Blobel | N/A | |
| Rabbit monoclonal anti-GAPDH | Cell Signaling Technology | Cat# 5G14; Cione# 14C1G; RRID:AB_1G69344B | |
| Rabbit polyclonal anti-FKBP12 antibody | Abcam | Cat# ab24373; RRID:AB_7323B3 | |
| Rabbit monoclonal anti-c-MYC antibody [Y69] | Abcam | Cat# ab32G72; RRID:AB_73165B | |
| Rabbit polyclonal anti-H3K27ac | Abcam | Cat# ab4729; RRID:AB_211B29 | |
| APC-R700 Mouse anti-Human CD45 Antibody | BDBiosciences | Cat# 566G41; RRID:AB_2744399 | |
| PerCP anti-mouse CD45 Antibody | Biolegend | Cat# 1G313G; RRID:AB_B93339 | |
| IgG from rabbit serum | Sigma-Aldrich | Cat#: IB14G; RRID:AB_1163661 | |
| Alexa Fluor® 680 Goat anti-mouse IgG (H+L) | Life Technologies | Product #A21G5B; Lot #1692967; RRID:AB_2535724 | |
| IRDye® 800CW Goat anti-Rabbit IgG Secondary Antibody | LI-COR | Product #926–3221, Lot #CB121G-G5 | |
| Rabbit polyclonal anti-H3K27me3 | Cell Signaling Tech | Cat#9733S; RRID:AB_2616G29 | |
| Mouse monoclonal anti-H3K14ac, clone 13HH3–1A5 | Millipore | Cat#: MABE351; RRID:AB_26B7B9G | |
| CD34-FITC, 581, ASR | Beckman Coulter | Cat# IM1B7GU; RRID:AB_1G639533 | |
| Human CD38 APCHIT2 | BDBiosciences | Cat# 56G9BG; RRID:AB_1G5B4324 | |
| APC anti-human CD135 (Flt-3/Flk-2) | Biolegend | Cat# 3133GB; RRID:AB_21G4B35 | |
| Rabbit polyclonal anti-FLI1 | Abcam | Cat# ab152B9; RRID:AB_3G1B25 | |
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| Chemicais, peptides, and recombinant proteins | |||
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| Halt Protease & Phosphatase Inhibitor Cocktail, EDTA- free (100×) | Thermo Fisher Scientific | Ref #78441, Lot #UF284419 | |
| Glycogen | Roche | Ref #10901393001, Lot #11651224 | |
| SuperScript II Reverse Transcriptase | Thermo Fisher Scientific | Cat# 18064014 | |
| AMPure XP | Beckman Coulter | A63880 | |
| Penicillin/ Streptomycin | Thermo Fisher Scientific | 15140122 | |
| Proteinase K | New England Biolabs | P8107S | |
| Puromycin dihydrochloride | Sigma-Aldrich | P8833 | |
| Blasticidin | Invitrogen | R21001 | |
| Geneticin Selective Antibiotic (G418 Sulfate) | Thermo Fisher Scientific | 10131035 | |
| Polyethylenimine, PEI | Polysciences, INC | 23966 | |
| OPTI-MEM | Thermo Fisher Scientific | 31985070 | |
| Hexadimethrine Bromide, Polybrene | Sigma-Aldrich | H9268 | |
| Dynabeads Protein A | Thermo Fisher Scientific | Ref #10002D, Lot #00651865 | |
| TRIzol Reagent | Thermo Fisher Scientific | 15596018 | |
| T4 DNA polymerase | New England Biolabs | M0203L | |
| T4 polynucleotide kinase | New England Biolabs | M0201L | |
| Agarose, Standard, Low Electroendosmosis (EEO) | Avantor | A426–07 | |
| 2-Mercaptoethanol | Sigma-Aldrich | M6250 | |
| 30% Acrylamide/Bis Solution, 37.5:1 | Bio-Rad | 1610158 | |
| 2XLaemmli Sample Buffer | Bio-Rad | 1610737 | |
| Dimethyl Sulfoxide | Sigma-Aldrich | D2650 | |
| Concanavalin A-coated Magnetic Beads | Bangs Laboratories | BP531 | |
| Digitonin | EMD Millipore | 300410 | |
| Spermidine | Sigma-Aldrich | S2501 | |
| dTAG-13/dTAG-47 | This study | N/A | |
| pA-MN | This study | N/A | |
| Spike-in DNA | Laboratory of Steven Henikoff | N/A | |
| Roche Complete Protease Inhibitor (EDTA-free) tablets | Sigma-Aldrich | 5056489001 | |
| DNA Polymerase I, Large (Klenow) Fragment | New England Biolabs | M0210 | |
| Formaldehyde 37% Solution | Avantor | 2106–01 | |
| RNase A | Thermo Fisher Scientific | EN0531 | |
| Phenol/Chloroform/Isoamyl Alcohol | Thermo Fisher Scientific | BP1752I400 | |
| NP-40 (Igepal CA-630) | Sigma | I8896 | |
| Mbol | New England Biolabs | R0147 | |
| Benzonase® Nuclease HC | Millipore | 71205 | |
| ANTI-FLAG® M2 Affinity Gel | Sigma-Aldrich | A2220 | |
| 3X FLAG® Peptide | Sigma-Aldrich | F4799 | |
| Trichostatin A | Sigma-Aldrich | T8552 | |
| rmIL3 | Peprotech | 213–13 | |
| rmIL6 | Peprotech | 216–16 | |
| rmSCF | Peprotech | 250–03 | |
| Methylcellulose-based Medium with Recombinant for Mouse | STEMCELL technologies | M3434 | |
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| Critical commercial assays | |||
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| CellTiter-Glo® Luminescent Cell Viability Assay | Promega | G7570 | |
| In-Fusion HD Cloning Kit | Takara Bio | 638909 | |
| 2× Phusion Master Mix | Thermo Scientific | F-548 | |
| Direct-zol RNA Miniprep Plus | Zymo Research | R2072 | |
| QuantSeq 30 mRNA-seq Library Prep Kit for Illumina | Lexogen | 015.96 | |
| Dead Cell Removal Kit | Miltenyi Biotec | 130–090-101 | |
| Agilent High Sensitivity DNA Kit | Agilent | 5067–4626 | |
| QIAquick PCR Purification Kit | QIAGEN | 28104 | |
| Quick-DNA Miniprep Kit | ZYMO Research | D3025 | |
| NucleoSpin Gel and PCR Clean-up Mini Kit | Macherey-Nagel | 740609.250 | |
| Aligent RNA 6000 Nano Kit | Aligent | 5067–1511 | |
| NEBNext® Library Quant Kit for Illumina | NEB | E7630 | |
| NEBNext® Ultra II RNA Library Prep Kit for Illumina® | NEB | E7770 | |
| NEBNext® Poly(A) mRNA Magnetic Isolation Module | NEB | E7490 | |
| TruSeq RNA Sample Prep Kit v.2 | Illumina | RS-122–2001 | |
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| Deposited data | |||
|
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| RNA-seq,ChIP-seq, 4C-seq and CUT&RUN data | This study | GSE157636 | |
| RNA-seq data | This study | GSE157249 | |
| ChIP-seq | Tarumoto et al., 2018 | GSE109493 | |
| ChIP-seq | Mohaghegh et al., 2019 | GSE123872 | |
| ChIP-seq | Poppe et al., 2017 | GSE89212 | |
| ChIP-seq and CUT&RUN | Krivtsov et al., 2019 | GSE127508 | |
| RNA-seq | Rathert et al., 2015 | GSE63782 | |
| RNA-seq and ATAC-seq | Corces et al., 2016 | GSE75384 | |
| SLAM-seq | Muharet al., 2018 | GSE100708 | |
| BET JQ1 AP-MS | Lambert et al., 2019 | MSV000081006 | |
| MS of rBRD4 domain | Lambert et al., 2019 | MSV000080986 | |
| MS of endogenouse BET IP-MS in HEK293T cells | Lambert et al., 2019 | MSV000082857 | |
| MS of endogenouse BET IP-MS in K562 cells | Lambert et al., 2019 | MSV000082859 | |
|
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| Experimental models: cell lines | |||
|
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| Human: MOLM-13 | DSMZ | ACC-554 | |
| Human: MV4–11 | ATCC | CRL-9591 | |
| Human: THP1 | ATCC | TIB-202 | |
| Human: NOMO1 | DSMZ | ACC-542 | |
| Human: HEL | ATCC | TIB-180 | |
| Human: OCI-AML3 | DSMZ | ACC-582 | |
| Human: SET-2 | DSMZ | ACC-608 | |
| Human: U937 | ATCC | CRL-1593.2 | |
| Human: K562 | ATCC | CCL-243 | |
| Human:JURKAT | ATCC | TIB-152 | |
| Human: SEM | DSMZ | ACC-546 | |
| Human: REH | ATCC | CRL-8286 | |
| Human: HEK293T | ATCC | CRL-3216 | |
| Human: ML2 | DSMZ | ACC-15 | |
| Human: A549 | ATCC | CCL-185 | |
| Human: HUH7 | JCRB | JCRB0403 | |
| Human: HUH1 | JCRB | JCRB0199 | |
| Human: HepG2 | ATCC | HB-8065 | |
| Human: SK-HEP1 | ATCC | HTB-52 | |
| Human: DMS114 | ATCC | CRL-2066 | |
| Human: NCI-H526 | ATCC | CRL-5811 | |
| Human: NCI-H82 | ATCC | HTB-175 | |
|
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| Experimental models: organisms/strains | |||
|
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| NOD scid gamma | JAX | Stock No: 005557 | |
| Constitutive-Cas9-GFP | JAX | Stock No: 026179 | |
|
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| Oligonucleotides | |||
|
| |||
| sgRNA sequence see Table S3 | This study | N/A | |
| qPCR primers see Table S3 | This study | N/A | |
| 4C-seq primers see Table S3 | This study | N/A | |
|
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| Recombinant DNA | |||
|
| |||
| LentiV_neo_empty | Tarumoto et al., 2018 | Addgene: 108101 | |
| LentiV_neo_ZMYND8 | This study | N/A | |
| LentiV_neo_ZMYND8 (N107A/F108A) | This study | N/A | |
| LentiV_neo_ZMYND8 (N248A) | This study | N/A | |
| LentiV_neo_ZMYND8 (F308A/F311A) | This study | N/A | |
| LentiV_MYC_PGK_blast | This study | N/A | |
| LentiV_neo_IRF8 | This study | N/A | |
| LentiV_Cas9_puro | Tarumoto et al., 2018 | N/A | |
| LRG(Lenti_sgRNA_EFS_GFP) | Tarumoto et al., 2018 | Addgene:65656 | |
| LRG2.1 | Tarumoto et al., 2018 | Addgene:108098 | |
| LRcherry2.1 | Tarumoto et al., 2018 | Addgene:108099 | |
| LentiV_neo_ZMYND8_FKBP12F36V-2×HA | This study | N/A | |
| LentiV_neo_FKBP12F36V-2×HA_IRF8 | This study | N/A | |
| pcDNA3_FLAG_ZMYND8 | This study | N/A | |
| pcDNA3_FLAG_BRD4L | Shen et al., 2015 | N/A | |
| GFP-ZMYND8 | Gong et al., 2015 | Addgene: 65401 | |
| pCRIS-PITChv2-Puro-dTAG vector | Nabet et al., 2018 | Addgene: 91793 | |
| pSL21-mCherry | Chen et al., 2021 | Addgene:164410 | |
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| Software and algorithms | |||
|
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| Bowtie2 v2.3.5 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | |
| BEDtools v2.28.0 | Quinlan and Hall, 2010 | https://bedtools.readthedocs.io/en/latest/ | |
| Samtools v1.1 | Li et al., 2009 | http://samtools.sourceforge.net | |
| HOMER v4 | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ | |
| bcl2fastq Conversion Software, v2.17 | Illumina, Inc. | https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html | |
| MACS2 v2.1 | Zhang et al., 2008 | https://github.com/macs3-project/MACS | |
| UCSC Genome Browser | UCSC | http://genome.ucsc.edu/ | |
| deepTools | Ramirez et al., 2016 | https://deeptools.readthedocs.io/en/develop/ | |
| Picard tools v1.96 | Broad Institute | https://github.com/broadinstitute/picard | |
| STAR v2.5.2 | Dobin et al., 2013 | https://github.com/alexdobin/STAR | |
| HTSeq, htseq-count, v0.6.1pl | Anders et al., 2015 | https://htseq.readthedocs.io/en/release_0.11.1/ | |
| R Bioconductor DESeq2 package v1.14.1 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html | |
| Blacklist | ENCODE | https://sites.google.com/site/anshulkundaje/projects/blacklists | |
| Juicer tools v1.7.6 | Durand et al., 2016 | https://github.com/aidenlab/juicer | |
| MSigDB v6.1 | Liberzon et al., 2015 | https://www.gsea-msigdb.org/gsea/msigdb/index.jsp | |
| Tophat2 | Kim et al., 2013 | http://ccb.jhu.edu/software/tophat/index.shtml | |
| Cufflinks | Trapnell et al., 2013 | http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/ | |
| deepTools | Ramirez et al., 2016 | https://deeptools.readthedocs.io/en/develop/index.html | |
| IGVtools, 2.4.10 | Broad Institute | https://software.broadinstitute.org/software/igv/igvtools | |
| FlowJo software, v10.0.7 | FlowJo | N/A | |
| GraphPad Prism 7 | GraphPad Software | N/A | |