REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-KDM3B, clone C69G2	Cell Signaling	Cat# 3314; RRID: AB_1264294
Anti-JMJD1B	Invitrogen	Cat# PA5-53459
Anti-G9a	Sigma	Cat# G6919; RRID: AB_262007
Anti-beta Actin	Millipore	Cat# MAB1501; RRID: AB626633
Anti-Actinin	Santa Cruz	Cat# sc-17829; RRID: AB_626633
Goat anti-mouse HRP	Biorad	Cat# 170-6516; RRID: AB11125547
Goat anti-rabbit HRP	GenScript	Cat# A00167
Anti-H3K9me1	Abcam	Cat# ab8896
Anti-H3K9me2	Abcam	Cat# ab1220
Anti-H3K9me3	Abcam	Cat# ab8898
Anti-CTCF, clone D31H2	Cell Signaling	Cat# 3418
Biological samples
Primary AML	Cihangir Duy 75	N/A
Chemicals, peptides, and recombinant proteins
Pierce Protease Inhibitor Tablets	Thermo Scientific	Cat# A32953
Pierce Phosphatase Inhibitor Tablets	Thermo Scientific	Cat# A32957
Propidium Iodide Solution	Sigma Aldrich	Cat# P4864
Doxorubicin	Sigma Aldrich	ab142052
Doxorubicin (Mouse study)	Selleckchem	Cat# E2516
Dulbecco’s Modified Eagles Medium – High Glucose	Sigma Aldrich	Cat# D5648
Roswell Park Memorial Institute Medium (RPMI)1640	Sigma Aldrich	Cat# R6504
Opti-Mem	Life Technologies	Cat# 31985070
Trypsin (0.25%) EDTA	Life Technologies	Cat# 2520056
L-Glutamine	Life Technologies	Cat# 25030-081
Penicillin and Streptomycin	Life Technologies	Cat# 15140122
Fetal Bovine Serum (FBS)	Gibco	Cat# 26140-079
Lipofectamine 3000	Life Technologies	Cat# L30000015
EHMTi	Jian Jin	UNC0642
KDM3i	Xu et al.52	JDI-12
Critical commercial assays
miRNeasy Mini Kit	Qiagen	Cat# 217004
Superscript IV 1st Strand System	Life Technologies	Cat# 18091050
CL-XPosure™ Film	Thermo Scientific	Cat# 34091
Lumi-Light Western Blotting Substrate	Roche	Cat# 12015200001
Pierce BCA Protein Assay	Thermo Scientific	Cat# 23223 and 23224
Protein A Dynabeads	Thermo Scientific	Cat# 10002D
Protein G Dynabeads	Thermo Scientific	Cat# 10004D
TruSeq ChIP Sample Prep Kit Set A (48 samples)	Illumina	Cat# 10748010
NextSeq® 500/550 High Output Kit v2 (75 cycles)	Illumina	Cat# FC-404-2005
Bac-to-Bac™ Baculovirus Expression System	Thermo Scientific	Cat# 10359016
Dead Cell Apoptosis Kits with Annexin V	Life Technologies	Cat# V13241
Deposited data
Raw ChIP-sequencing	This paper	GEO: GSE210480
KDM3B ChIP-seq	Li et al.51	GEO: GSE71885
RPE CTCF ChIP-seq	ENCODE	GEO: GSM749673
GM12878 CTCF ChIP-seq	ENCODE	GEO: GSM733752
H1 CTCF ChIP-seq	ENCODE	GEO: GSM733672
bronchial_epithelial CTCF ChIP-seq	ENCODE	GEO: GSM749779
Bcell CTCF ChIP-seq	ENCODE	GEO: GSM1003474
HL-60 CTCF ChIP-seq	ENCODE	GEO: GSM749688
HCT116 CTCF ChIP-seq	ENCODE	GEO: GSM1022652
Experimental models: Cell lines
RPE-hTERT1	Nick Dyson	N/A
U937	FCCC Cell Culture Facility	CRL-1593.2
HL60	ATCC	CCL-240
KG1a	ATCC	CCL-246.1
HSPC	Cihangir Duy; 75	N/A
Experimental models: Organisms/strains
Mouse: C57BL/6 / 129/Sv	Jackson Labs	Strain# 101043
Oligonucleotides
See Table S3 for Oligonucleotides used	This paper	N/A
Recombinant DNA
Halo-CTCF	Promega	Cat# FHC01807
Halo-KDM3B	Promega	Cat# FHC05559
Halo-Tag Alone	Promega	Cat# G6591
MLL-1 Probe	Oxford Gene Technology	Cat# LPH 506-A
MLL breakapart	Oxford Gene Technology	Cat# LPH 013-A
AML1 breakapart	Oxford Gene Technology	Cat# LPH 027-SA
BCL6 breakapart	Oxford Gene Technology	Cat# LPH 035-SA
EVL1 breakapart	Oxford Gene Technology	Cat# LPH 036-SA
TCRB breakapart	Oxford Gene Technology	Cat# LPH 048-SA
MLLT1	Oxford Gene Technology	Cat# LPH 508-A
MLLT3	Oxford Gene Technology	Cat# LPH 509-A
Chromosome 11 Alpha Satellite Red	Oxford Gene Technology	Cat# LPE 011R-A
E2A breakapart	Oxford Gene Technology	Cat# LPH 019-SA
5q del probe	Oxford Gene Technology	Cat# LPH 024
19p probe	Oxford Gene Technology	Cat# LPT19 PR-A
NMYC/LAF4 probe	Oxford Gene Technology	Cat# LPS-009A
MLL adjacent probe (CD3)	Empire Genomics	RPCI-11 215H18
Kmt2a/Chr9 Mouse	Empire Genomics	Mouse KMT2A-Chr09
Software and algorithms
Scaffold 6.0	3i-intelligent imaging Innovations	https://www.intelligent-imaging.com/slidebook
BWA 0.7.13	Li et al.78	https://biobwa.sourceforge.net/bwa.shtml
DeepTools 2.4.3	Ramirez et al.79	https://deeptools.readthedocs.io/en/develop/content/installation.html
HOMER v4.10.3	Heinz et al.80	http://homer.ucsd.edu/homer/
DiffBind	Ross-Innes et al.81	https://bioconductor.org/packages/release/bioc/html/DiffBind.html