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-DNA-RNA Hybrid [S9.6] Antibody | Kerafast | Cat# ENH001, RRID:AB_2687463 |
| 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-GST antibody, rabbit polyclonal | Cell Signaling Technology | Cat# 2622, RRID:AB_331670 |
| Anti-CTCF antibody, rabbit polyclonal | Cell Signaling Technology | Cat# 2899, RRID:AB_2086794 |
| Anti-SA1 antibody, goat polyclonal | Abcam | Cat# ab4457, RRID:AB_2286589 |
| Anti-SA2 antibody, goat polyclonal | Abcam | Cat# ab4464, RRID:AB_304472 |
| Anti-RAD21 antibody, rabbit polyclonal | Abcam | Cat# ab992, RRID:AB_2176601 |
| Anti-DHX9 antibody, mouse monoclonal | Sigma-Aldrich | Cat# WH0001660M1, RRID:AB_1841284 |
| Anti-RPA1 antibody, rabbit monoclonal | Abcam | Cat# ab79398, RRID:AB_1603759 |
| Anti-PARP1 antibody, rabbit polyclonal | Sigma-Aldrich | Cat# AV33754, RRID:AB_1854978 |
| Anti-DDX5 antibody, rabbit polyclonal | Cell Signaling Technology | Cat# 4387, RRID:AB_2090733 |
| Anti-Lamin B1 antibody, rabbit monoclonal | Cell Signaling Technology | Cat# 13435, RRID:AB_2737428 |
| Anti-SRSF1 antibody, rabbit polyclonal | Thermo Fisher Scientific | Cat# PA5-30220, RRID:AB_2547694 |
| Anti-MCM3 antibody, rabbit polyclonal | Cell Signaling Technology | Cat# 4012, RRID:AB_2235150 |
| Anti-NPM1 Antibody, mouse monoclonal | Novus Biologicals | Cat# NB600-1030, RRID:AB_10001674 |
| Mouse IgG Isotype Control antibody | Thermo Fisher Scientific | Cat# 31903, RRID:AB_10959891 |
| Normal Rabbit IgG antibody | Cell Signaling Technology | Cat# 2729, RRID:AB_1031062 |
| Anti-HDAC1, rabbit polyclonal | Abcam | Cat# ab7028, RRID:AB_305705 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Lipofectamine 3000 reagent | Thermo Fisher Scientific | Cat#L3000-008 |
| Proteinase K | Thermo Fisher Scientific | Cat#25530049 |
| RNase A | Thermo Fisher Scientific | Cat#EN0531 |
| RNase H | New England Biolabs | Cat#M0297L |
| DpnII | New England Biolabs | Cat#R0543L |
| 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 |
| Dynabeads™ M-280 Streptavidin | Thermo Fisher Scientific | Cat#11206D |
| 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 |
| Pierce™ Glutathione Agarose | Thermo Fisher Scientific | Cat#16101 |
| D-Biotin | Thermo Fisher Scientific | Cat#B20656 |
| T5 exonuclease | New England Biolabs | Cat#M0363 |
| TRI Reagent | Sigma-Aldrich | Cat#93289 |
| Superase-in | Thermo Fisher Scientific | Cat#AM2696 |
| Nonidet P40 | Millipore | Cat#11332473001 |
| IGEPAL® CA-630 | Millipore | Cat#I8896 |
| laemmli sample buffer (4X) | Thermo Fisher Scientific | Cat#84788 |
| BrUTP | Biotium | Cat#40026 |
| One-Step Blue® Protein Gel Stain | Biotium | Cat#21003 |
| 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 |
| AmpliScribe™ T7-Flash™ Biotin-RNA Transcription Kit | Lucigen | Cat#ASB71110 |
| 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 |
| TruSeq Stranded mRNA Library Prep | Illumina | Cat# 20020594 |
| TruSeq ChIP Library Preparation Kit | Illumina | Cat# IP-202-1012 |
| Arima-HiC Kit | Arima | Cat#A410030 |
| KAPA Hyper Prep Kit | KAPA | Cat # KK8500, KK4824 and KK8502 |
| NEBNext® DNA Library Prep Master Mix Set for Illumina | New England Biolabs | Cat # E6040 |
| NEBNext Ultra II | New England Biolabs | Cat # 7645S |
| NEBNext Multiplex Oligos for Illumina Primer set 1 | New England Biolabs | Cat # E7335S |
| NEBNext Multiplex Oligos for Illumina Primer set 2 | New England Biolabs | Cat # E7500S |
| SureSelectXT Mouse All Exon | Agilent | Cat # 5190-4641 |
| pGEM®-T Easy Vector Systems | Promega | Cat#A137A |
| Herculase II Fusion Polymerase kit | Agilent | Cat#600677 |
| Nimblegen SeqCap EZ HE-oligo kit A | Roche | Cat#06777287001 |
| Nimblegen SeqCap EZ HE-oligo kit B | Roche | Cat#06777317001 |
| Nimblegen SeqCap EZ Accessory kit v2 | Roche | Cat#07145594001 |
| Nimblegen SeqCap EZ Hybridisation and wash kit | Roche | Cat#05634261001 |
| KAPA Library Quantification Complete Kit (Universal) | KAPA | Cat#KK4824 |
| Qubit High Sensitivity Assay kit | Thermo Fisher Scientific | Cat#Q32854 |
| NEBNext Ultra II Directional RNA Library Prep kit | New England Biolabs | Cat#E7765 |
| SingleShot™ SYBR® Green One-Step Kit | Bio-Rad Laboratories | Cat#1725095 |
| Deposited Data | ||
| RNA-seq in WT vs HOTTIP−/− MOLM13 cells | (Luo et al., 2019) | GEO: GSE114981 |
| ATAC-seq in WT vs HOTTIP−/− MOLM13 cells | (Luo et al., 2019) | GEO: GSE114981 |
| CHIRP-seq of WT vs HOTTIP−/− MOLM13 cells | (Luo et al., 2019) | GEO: GSE114981 |
| CHIRP-seq of WT vs Hottip-Tg LK cells | This paper | GEO: GSE165049 |
| H3K4me3/H3K27me3 ChIP-seq of WT vs HOTTIP−/− MOLM13 cells | (Luo et al., 2019) | GEO: GSE114981 |
| H3K4me3/H3K27me3 ChIP-seq of WT, CBS-u2−/−, CBS-u2RH MOLM13 cells | This paper | GEO: GSE165049 |
| RNA-seq of WT vs Hottip-Tg mice LSK cells | This paper | GEO: GSE114981 |
| ATAC-seq of WT vs Hottip-Tg mice LSK cells | This paper | GEO: GSE114981 |
| CTCF/SA1/SA2/RAD21 ChIP-seq of WT vs HOTTIP−/− MOLM13 cells | This paper | GEO: GSE165049 |
| CTCF ChIP-seq of WT vs Hottip-Tg LK cells | This paper | GEO: GSE165049 |
| DRIP-seq of WT vs HOTTIP−/− MOLM13 cells | This paper | GEO: GSE165049 |
| DRIPc-seq of WT vs HOTTIP−/− MOLM13 cells | This paper | GEO: GSE165049 |
| Single cell RNA-seq of WT vs Hottip-Tg mice | This paper | GEO: GSE165049 |
| HiC-seq of WT vs HOTTIP−/− MOLM13 cells | (Luo et al., 2019) | GEO: GSE114981 |
| HiC-seq of WT vs Hottip-Tg mice LSK cells | This paper | GEO: GSE165049 |
| GRO-seq of WT vs HOTTIP−/− MOLM13 cells | This paper | GEO: GSE165049 |
| RNA-seq of WT vs CBS-u2RH MOLM13 cells | This paper | GEO: GSE165049 |
| NG-Capture-C-seq of WT, HOTTIP−/−, CBS-u2−/−, CBS-u2RH MOLM13 cells | This paper | GEO: GSE165049 |
| Experimental Models: Cell Lines | ||
| MOLM-13 | DSMZ | Cat# ACC-554, RRID:CVCL_2119 |
| HEK293T | ATCC | Cat# CRL-3216, RRID:CVCL_0063 |
| OCI-AML2 | DSMZ | Cat# ACC-99, RRID:CVCL_1619 |
| OCI-AML3 | DSMZ | Cat# ACC-582, RRID:CVCL_1844 |
| Experimental Models: Organisms/Strains | ||
| Hottip-Transgenic mouse | (Luo et al., 2019) | N/A |
| Xenograft AML mouse model | This paper | N/A |
| Oligonucleotides | ||
| sgRNAs | This paper | Upon request |
| RT-qPCR primers | This paper | Upon request |
| ChIP-qPCR primers | This paper | Upon request |
| ATAC primers | This paper | Upon request |
| CHIRP Probes | This paper | Upon request |
| RIDP Probes | This paper | Upon request |
| NG-Capture-C-biotin oligos | This paper | Upon request |
| Cy3 or Cy5 labelled oligos | This paper | Upon request |
| 3C primers | This paper | Upon request |
| 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 |
| pFRT-TODestGFP_RNAseH1 | (Lu et al., 2018) | Addgene Plasmid # 65784; RRID:Addgene_65784 |
| ppyCAG_RNaseH1_D210N | (Chen et al., 2017) | Addgene Plasmid # 111904; RRID:Addgene_ 111904 |
| human beta-catenin pcDNA3 | (Kolligs et al., 1999) | Addgene Plasmid # 16828; RRID:Addgene_ 16828 |
| pLenti-CMV-FLAG-puro | (Agrotis et al., 2019) | Addgene Plasmid # 123223; RRID:Addgene_ 123223 |
| pMD2.G | Addgene | Addgene Plasmid # 12259; RRID:Addgene_12259 |
| pBlueScript II SK | Addgene | Addgene Plasmid #212205; RRID:Addgene_212205 |
| HS321/45-vav-HOTTIP vector | (Luo et al., 2019) | N/A |
| pTre-Tight-luciferase-HOTTIP | Addgene | Addgene Plasmid #65490; RRID:Addgene_65490 |
| psPAX2 | Addgene | Addgene Plasmid #12260; RRID:Addgene_12260 |
| pGEX-5X-1 | Addgene | Addgene Plasmid # 27-4584-01; RRID:Addgene_ 27-4584-01 |
| Software and Algorithms | ||
| TopHat/2.0.13 | (Trapnell et al., 2012) | https://ccb.jhu.edu/software/tophat/ |
| Bowtie2/2.2.9 | (Langmead and Salzberg, 2012) | http://bowtiebio.sourceforge.net/bowtie2/ |
| R/3.6.1 | N/A | https://www.r-project.org/ |
| Cufflinks/2.2.1 | (Trapnell et al., 2010) | http://cole-trapnell-lab.github.io/cufflinks/ |
| Cuffdiff/2.2.1 | (Trapnell et al., 2010) | http://cole-trapnell-lab.github.io/cufflinks/ |
| Integrated Genomic Viewer (version 2.4.19) | (Robinson et al., 2011) | http://software.broadinstitute.org/ |
| Deeptools/3.1.3 | (Ramirez et al., 2014) | https://deeptools.github.io/ |
| Gene Set Enrichment Analysis (GSEA) (4.0.0) | (Subramanian et al., 2005) | http://software.broadinstitute.org/gsea/ |
| chromVAR(3.10) | (Schep et al., 2017) | https://bioconductor.org/packages/release/bioc/html/chromVAR.html |
| Homer/4.10 | (Heinz et al., 2010) | http://homer.ucsd.edu/homer/index.html |
| Juicer (version 1.6) | (Durand et al., 2016b) | https://github.com/aidenlab/juicer/ |
| Juicebox(version 2.1.4) | (Durand et al., 2016a) | http://aidenlab.org/juicebox/ |
| HiCExplorer (3.5.3) | (Wolff et al., 2020) | https://hicexplorer.readthedocs.io/en/latest/ |
| QmRLFS-finder (version v1.4) | (Jenjaroenpun et al., 2015) | http://rloop.bii.a-star.edu.sg/?pg=qmrlfs |
| capC-MAP(1.1.3) | (Hughes et al., 2014, Buckle et al., 2019) | https://capc-map.readthedocs.io/en/latest/ |