KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-H3K4me3 antibody, rabbit monoclonal | Millipore | Cat#04–745; RRID:AB_1163444 |
| Anti-H3K27me3 antibody, rabbit polyclonal | Millipore | Cat#07–449; RRID:AB_310624 |
| Anti-H3K9me2 antibody, rabbit polyclonal | Millipore | Cat#17–681, RRID:AB_1977531 |
| Anti-H3K79me2 antibody, rabbit polyclonal | Abcam | Cat#ab3594; RRID:AB_303937 |
| Anti-CD45 antibody, rabbit polyclonal | Abcam | Cat#ab10559, RRID:AB_442811 |
| Anti-Ly-6A/E (Sca-1) antibody, mouse monoclonal | BioLegend | Cat#108111, RRID:AB_313348 |
| Anti-CD117 (c-kit) antibody, mouse monoclonal | BioLegend | Cat#135135, RRID:AB_2632808 |
| Anti-CD34 antibody, mouse monoclonal | BD Biosciences | Cat#553733, RRID:AB_395017 |
| Anti-CD135 antibody, mouse monoclonal | BD Biosciences | Cat#558995, RRID:AB_397174 |
| Anti-CD16 antibody, mouse monoclonal | BD Biosciences | Cat#555405, RRID:AB_395805 |
| Anti-KMT2A/MLL antibody, rabbit polyclonal | Novus Biologicals | Cat#NB600–248, RRID:AB_2145479 |
| Anti-WDR5 antibody, mouse monoclonal | Abcam | Cat#ab56919, RRID:AB_946146 |
| Anti-DOT1L antibody, rabbit polyclonal | Novus Biologicals | Cat# NB100–40845, RRID:AB_789636 |
| Anti-p-STAT5A, rabbit polyclonal | Cell Signaling Technology | Cat# 9351, RRID:AB_2315225 |
| Anti-STAT5A, rabbit monoclonal | Cell Signaling Technology | Cat# 94205, RRID:AB_2737403 |
| Anti-HDAC1, rabbit polyclonal | Abcam | Cat# ab7028, RRID:AB_305705 |
| Anti-RUNX1, rabbit polyclonal | Abcam | Cat# ab23980, RRID:AB_2184205 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Lipofectamine 3000 reagent | Thermo Fisher Scientific | Cat#L3000–008 |
| Proteinase K | Thermo Fisher Scientific | Cat#25530049 |
| Alt-R® S.p. Cas9 Nuclease 3NLS | Integrated DNA Technologies | Cat#1074181 |
| Alt-R® CRISPR-Cas9 tracrRNA | Integrated DNA Technologies | Cat#1072532 |
| Alt-R® Cas9 Electroporation Enhancer | Integrated DNA Technologies | Cat#1075915 |
| Protease inhibitor Cocktail | Abcam | Cat#ab65621 |
| Dynabeads™ Protein G | Thermo Fisher Scientific | Cat#10003D |
| Dynabeads™ Protein A | Thermo Fisher Scientific | Cat#10001D |
| Dynabeads™ MyOne™ Streptavidin C1 | Thermo Fisher Scientific | Cat#65001 |
| SUPERase• In™ RNase Inhibitor | Thermo Fisher Scientific | Cat#AM2694 |
| RNaseOUT™ Ribonuclease Inhibitor | Thermo Fisher Scientific | Cat#10777019 |
| Pierce Protease Inhibitor Tablets | Thermo Fisher Scientific | Cat#A32963 |
| TURBO™ DNase | Thermo Fisher Scientific | Cat#AM2238 |
| AMPure XP beads | Beckman Coulter | Cat#A63881 |
| Critical Commercial Assays | ||
| RNeasy mini-isolation kit | QIAGEN | Cat#74106 |
| Neon™ Transfection System Kit | Thermo Fisher Scientific | Cat#MPK1025 |
| QIAquick Gel Extract kit | QIAGEN | Cat#28706 |
| Alt-R® CRISPR-Cas9 Control Kit | Integrated DNA Technologies | Cat#1072554 |
| mirVana PARIS kit | Thermo Fisher Scientific | Cat#AM1556 |
| Superscript II reverse Transcriptase | Thermo Fisher Scientific | Cat#18064014 |
| QIAquick PCR purification kit | QIAGEN | Cat#28106 |
| QIAprep Spin Miniprep Kit | QIAGEN | Cat#27106 |
| QIAGEN Plasmid Plus Maxi Kit | QIAGEN | Cat#12965 |
| Nextera DNA Library Preparation Kit | illumina | Cat#FC-121–1030 |
| Arima-HiC Kit | Arima | Cat#A410030 |
| KAPA Hyper Prep Kit | KAPA | Cat # KK8500, KK4824 and KK8502 |
| SureSelectXT Mouse All Exon | Agilent | Cat # 5190–4641 |
| pGEM®-T Easy Vector Systems | Promega | Cat#A137A |
| SingleShot™ SYBR® Green One-Step Kit | Bio-Rad Laboratories | Cat#1725095 |
| Deposited Data | ||
| RNA-seq in WT vs HOTTIP-KO MOLM13 | This paper | GEO: GSE114981 |
| ATAC-seq in WT vs HOTTIP-KO MOLM13 | This paper | GEO: GSE114981 |
| RNA-seq in WT vs CBS7/9-KO MOLM13 | (Luo et al., 2018) | GEO: GSE113191 |
| CHIRP-seq of WT vs HOTTIP-KO MOLM13 | This paper | GEO: GSE114981 |
| ChIP-seq of WT vs HOTTIP-KO MOLM13 | This paper | GEO: GSE114981 |
| LSK RNA-seq of WT vs Hottip-Tg mice | This paper | GEO: GSE114981 |
| LSK ATAC-seq of WT vs Hottip-Tg mice | This paper | GEO: GSE114981 |
| LT-HSC RNA-seq of WT vs Hottip-Tg mice | This paper | GEO: GSE114981 |
| ST-HSC RNA-seq of WT vs Hottip-Tg mice | This paper | GEO: GSE114981 |
| LT-HSC ATAC-seq of WT vs Hottip-Tg mice | This paper | GEO: GSE114981 |
| ST-HSC ATAC-seq of WT vs Hottip-Tg mice | This paper | GEO: GSE114981 |
| HiC-seq of WT vs HOTTIP-KO MOLM13 | This paper | GEO: GSE114981 |
| HiC-seq of HOTTIP-KO MOLM13 | This paper | GEO: GSE114981 |
| HiC-seq of CBS7/9-KO MOLM13 | This paper | GEO: GSE114981 |
| HiC-seq of CBS7/9-KO-VP-HT MOLM13 | This paper | GEO: GSE114981 |
| Mouse whole exome sequencing | This paper | GEO: GSE114981 |
| Experimental Models: Cell Lines | ||
| MOLM-13 | DSMZ | Cat# ACC-554, RRID:CVCL_2119 |
| HEK293T | ATCC | Cat# CRL-3216, RRID:CVCL_0063 |
| OCI-AML3 | DSMZ | Cat# ACC-582, RRID:CVCL_1844 |
| Experimental Models: Organisms/Strains | ||
| Hottip-Transgenic mouse | This paper | N/A |
| Xenograft AML mouse model | This paper | N/A |
| Oligonucleotides | ||
| sgRNAs | This paper | see Table S4 |
| RT-qPCR primers | This paper | see Table S4 |
| ChIP-PCR primers | This paper | see Table S4 |
| crRNAs | This paper | see Table S4 |
| ATAC primers | This paper | see Table S4 |
| CHIRP Probes | This paper | see Table S4 |
| Recombinant DNA | ||
| pL-CRISPR.EFS.GFP | Heckl et al., 2014 | Addgene Plasmid #57818; RRID:Addgene_57818 |
| pLKO5.sgRNA.EFS.tRFP | Heckl et al., 2014 | Addgene Plasmid #57824; RRID:Addgene_57824 |
| lentiCRISPR v2 | Sanjana et al., 2014 | Addgene Plasmid # 52961; RRID:Addgene_52961 |
| pHR-SFFV-dCas9-BFP-KRAB | Gilbert et al., 2013 | Addgene Plasmid #46911; RRID:Addgene_46911 |
| pAC94-pmax-dCas9VP160–2A-puro | Cheng et al., 2013 | Addgene Plasmid #48226; RRID:Addgene_48226 |
| pMD2.G | Will et al., 2015 | Addgene Plasmid # 12259; RRID:Addgene_12259 |
| psPAX2 | Will et al., 2015 | Addgene Plasmid #12260; RRID:Addgene_12260 |
| pLKO5-SgHottip-GFP-CRISPRi | This paper | Addgene Plasmid # 134989 |
| pLKO5-SgHottip-GFP-CRISPRa | This paper | Addgene Plasmid # 134990 |
| Software and Algorithms | ||
| TopHat | (Trapnell et al., 2012) | https://ccb.jhu.edu/software/tophat/ |
| Bowtie2 | (Langmead and Salzberg, 2012) | http://bowtiebio.sourceforge.net/bowtie2/ |
| R | N/A | https://www.r-project.org/ |
| Cufflinks | (Trapnell et al., 2010) | http://cole-trapnell-lab.github.io/cufflinks/ |
| Cuffdiff | (Trapnell et al., 2010) | http://cole-trapnell-lab.github.io/cufflinks/ |
| Integrated Genomic Viewer | (Robinson et al., 2011) | http://software.broadinstitute.org/ |
| Deeptools | (Ramirez et al., 2014) | https://deeptools.github.io/ |
| Gene Set Enrichment Analysis (GSEA) | (Subramanian et al., 2005) | http://software.broadinstitute.org/gsea/ |
| chromVAR | (Schep et al., 2017) |
https://bioconductor.org/packages/release/bioc/ html/chromVAR.html |
| Homer | (Heinz S et al., 2010) | http://homer.ucsd.edu/homer/index.html |
| Juicer | (Neva C. Durand, 2016) | https://github.com/aidenlab/juicer/ |
| Juicebox | (Neva C. Durand, 2016) | http://aidenlab.org/juicebox/ |