REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-CTCF	Millipore	Cat# 07-729; RRID: AB_441965
Rabbit polyclonal anti-CTCF	Abcam	Cat# ab128873; RRID: AB_11144295
Rabbit polyclonal anti-CTCF	Active motif	Cat# 61311; RRID: AB_2614975
Rabbit polyclonal anti-HaloTag	Promega	Cat# G9281; RRID: AB_713650
Rabbit monoclonal anti-FLAG	Sigma-Aldrich	Cat# F1804; RRID: AB_262044
Rabbit monoclonal anti-BRD2	Cell Signaling Technology	Cat# 5848; RRID: AB_10835146
Mouse monoclonal anti-GAPDH	Proteintech	Cat# 60004-1-Ig; RRID: AB_2107436
Mouse monoclonal anti-Actin	Proteintech	Cat# 66009-1-Ig; RRID: AB_2687938
Donkey anti-Rabbit IgG, Alexa Fluor 488	Invitrogen	Cat# A-21206; RRID: AB_2535792
Donkey anti-Rabbit IgG, Alexa Fluor 568	Invitrogen	Cat# A-10042; RRID: AB_2534017
Rabbit IgG HRP Linked Whole Ab	Sigma-Aldrich	Cat# GENA934-1ML; RRID: AB_2722659
Mouse IgG HRP Linked Whole Ab	Sigma-Aldrich	Cat# GENXA931-1ML; RRID: AB_772209
Bacterial and virus strains
TransT1 Chemically Competent Cell	Transgene	Cat# CD501-02
Transetta (DE3) Chemically Competent Cell	Transgene	Cat# CD801-02
Chemicals, peptides, and recombinant proteins
Halotag-JF549 ligand	Promega	Cat# GA1110
Indole-3-acetic acid	Sigma-Aldrich	Cat# I5148
GSK3b inhibitor CHIR99021	Selleck Chemicals	Cat# S2924
MEK inhibitor PD0325901	Selleck Chemicals	Cat# S1036
YOYO-1	Thermo Fisher	Cat# Y3601
SYBR Safe	Thermo Fisher	Cat# S33102
mLIF	Millipore	Cat# ESG1107
Critical commercial assays
Lipofectamine 2000	Mei5bio	Cat# MF135-1
Lipofectamine RNAiMAX	Thermo Fisher	Cat# 13778075
Deposited data
Microscopy images and blots scans data	This paper	Mendeley data: https://doi.org/10.17632/ssj66hy8sd.1
Experimental models: Cell lines
HEK293T cells	ATCC	CRL-3216
U2OS cells	ATCC	HTB-96
V6.5 murine embryonic stem cells	Richard A. Young laboratory	N/A
mESC CTCF-GFP-mAID	Wei Xie laboratory	N/A
Oligonucleotides
Guide RNA sequences (sgRNAs) for Chr3q29 loci: TGATATCACAG	This Paper	N/A
Primers for plasmid constructs, see Table S5	This Paper	N/A
Primers for qPCR, see Table S5	This Paper	N/A
EMSA C-MYC probes: CTGCTGCCAGTAGAGGGCACACTTA	This Paper	N/A
EMSA NC probes: TCTCCTATGACTCGTCCAT	This Paper	N/A
Sence-CTCF-siRNA: GCGCUCUAAGAAAGAAGAUUCCUCU	This Paper	N/A
Antisence-CTCF-siRNA: AGAGGAAUCUUCUUUCUUAGAGCGC	This Paper	N/A
Sence-Ctrl-siRNA: CGUACGCGGAAUACUUCGATT	This Paper	N/A
Antisence-Ctrl-siRNA: UCGAAGUAUUCCGCGUACGTT	This Paper	N/A
Recombinant DNA
pHR-mCherry-CRY2	Shin et al. (2017)	Addgene Plasmid #101221
pHR-FUSN-mCherry-CRY2	Shin et al. (2017)	Addgene Plasmid #101223
pHR-CTCF(DBD)-mCherry-CRY2	This Paper	N/A
pHR-CTCF(RBD)-mCherry-CRY2	This Paper	N/A
pHR-CTCF(NTD)-mCherry-CRY2	This Paper	N/A
pHR-CTCF(R-I)-mCherry-CRY2	This Paper	N/A
pHR-CTCF(K-I)-mCherry-CRY2	This Paper	N/A
pHR-CTCF(H-I)-mCherry-CRY2	This Paper	N/A
pHR-BCL6(DBD)-mCherry-CRY2	This Paper	N/A
pHR-GATA3(DBD)-mCherry-CRY2	This Paper	N/A
pHR-P53(DBD)-mCherry-CRY2	This Paper	N/A
pHR-YY1(DBD)-mCherry-CRY2	This Paper	N/A
pET28a-SUMO-eGFP	This Paper	N/A
pET28a-SUMO-CTCF(DBD)-eGFP	This Paper	N/A
pET28a-SUMO-CTCF(NTD)-eGFP	This Paper	N/A
pET28a-SUMO-CTCF(RBD)-eGFP	This Paper	N/A
pET28a-SUMO-meGFP	This Paper	N/A
pET28a-CTCF(DBD)-meGFP	This Paper	N/A
pET28a-SUMO-CTCF(DBD)-meGFP	This Paper	N/A
pX332-eGFP	This Paper	N/A
pX332-BRD2-eGFP	This Paper	N/A
pX332-CHD8-eGFP	This Paper	N/A
pX332-BRD3-eGFP	This Paper	N/A
pX332-OCT4-eGFP	This Paper	N/A
pX332-NANOG-eGFP	This Paper	N/A
pX332-SOX2-eGFP	This Paper	N/A
pX332-Halo-eGFP	This Paper	N/A
pIHLME	Yao et al. (2010)	N/A
pIHLIE	Yao et al. (2010)	N/A
phRG-TK	Yuanchao Xue laboratory	N/A
pcDNA-CTCF-2xFLAG	This Paper	N/A
pcDNA-CTCF(R377C)-2xFLAG	This Paper	N/A
pcDNA-CTCF(R377H)-2xFLAG	This Paper	N/A
pLH-sgRNA-Chr3	This Paper	N/A
pHAGE-TO-dCas9-3xmcherry	Ma et al., 2015	Addgene Plasmid #64108
pHAGE-TO-dCas9-3xmcherry-CTCF	This Paper	N/A
pHAGE-TO-dCas9-3xmcherry-CTCF(dDBD)	This Paper	N/A
Software and algorithms
ImageJ	National Institutes of Health (NIH)	https://imagej.nih.gov/ij/
Volocity (v.6.3)	PerkinElmer	https://www.perkinelmer.com/
FrapBot	(Kohze et al., 2017)	http://frapbot.kohze.com/
GraphPad (v.7)	Prism	https://www.graphpad.com/scientific-software/prism
Bowtie2 (v2.3.5.1)	Langmead and Salzberg. (2012)	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
MACS2 (v2.2.5)	Zhang et al. (2008)	https://github.com/taoliu/MACS
deeptools (v3.4.3)	Ramirez et al. (2016)	https://deeptools.readthedocs.io/en/develop/
Homer (v4.10)	Heinz et al. (2010)	http://homer.ucsd.edu/homer/motif/
BEDTools (v2.27.1)	Quinlan and Hall. (2010)	https://github.com/arq5x/bedtools2
Other
PerkinElmer UltraView VoX spinning disk confocal microscopy	Nikon	N/A
Nikon A1RSi confocal microscopy	Nikon	N/A
DeltaVision OMX System	GE Healthcare	N/A
JASPAR	Khan et al. (2018)	https://jaspar.genereg.net/
COSMIC	Tate et al. (2019)	https://cancer.sanger.ac.uk/cosmic
hESC CTCF ChIP-seq	GSE69646	Ji et al. (2016)
mESC CTCF ChIP-exo	GSE98671	Nora et al. (2017)
mESC ChIP-seq datasets (SMC1, OCT4, NANOG, and CBP)	GSE44286	Whyte et al. (2013)