REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
rabbit polyclonal antibody anti-GTF3C2	This paper	NA
mouse monoclonal antibody anti-GTF3C2	Abcam	RRID:AB_2043034
rabbit polyclonal antibody anti-BDP1	Wang and Roeder, 1997, Weser et al., 2004	NA
rabbit polyclonal antibody anti-RPC39	Wang and Roeder, 1997, Weser et al., 2004	NA
rabbit polyclonal antibody anti-H3K18ac	Active motif	RRID:AB_2793308
rabbit polyclonal antibody anti-CTCF	Millipore	RRID:AB_441965
rabbit monoclonal antibody anti-CTCF	Abcam	ab128873
rabbit polyclonal antibody anti-Pol II	Cell Signaling	(NTD) (D8L4Y, Cat# 14958 RRID:AB_2687876)
rabbit affinity-purified anti-GTF3C5/TFIIIC63	Bethyl	RRID:AB_890669
rabbit affinity-purified anti-GTF3C1/TFIIIC220	Novus Biologicals	RRID:AB_922616
rabbit affinity-purified anti-GTF3C4/TFIIIC90	Abcam	RRID:AB_1269036
mouse Monoclonal antibody anti-tubulin	Sigma	RRID:AB_477593
rabbit anti-GTF3C1/TFIIIC220 Antibody, Affinity Purified ChIP	Bethyl	RRID:AB_938038
rabbit anti-GTF3C1/TFIIIC220 Antibody, Affinity Purified WB	Bethyl	RRID:AB_938042
mouse monoclonal [102C1a] to ADNP	Abcam	RRID:AB_879525
Rabbit polyclonal HA tag antibody	Abcam	RRID:AB_307019
rabbit affinity-purified anti-EP300	Santa Cruz	RRID:AB_2231120-Lot: I2815
rabbit affinity-purified anti-EP300	Santa Cruz	RRID:AB_2293429-Lot: J0915
Rabbit affinity-purified anti-H3K9ac	Active Motif	RRID:AB_2561017-Lot16918002
Mouse Monoclonal anti-H3K27ac	Millipore	RRID:AB_1977529-Lot.2626032
Rabbit polyclonal to Histone H1.2	Abcam	RRID:AB_2117983
Horseradish peroxidase conjugated anti-mouse	Amersham	NA931V
Horseradish peroxidase conjugated anti-rabbit	Amersham	NA934V
Anti-DYKDDDDK resin	Genscript	L00432
Anti-HA Agarose	Pierce	26181
Bacterial and Virus Strains
One Shot Stbl3 Chemically Competent E. coli	Invitrogen	C7373-03
Chemicals, Peptides, and Recombinant Proteins
RPMI Red phenol	GIBCO	42401-018
RPMI No Phenol Red	GIBCO	32404-014
DMEM Phenol Red	GIBCO	41965-039
DMEM Phenol Red	GIBCO	21063-029
DMEM/F12 Phenol Red	GIBCO	11330-032
DMEM/F12 No Phenol Red	GIBCO	11039-021
EMEM Phenol Red	GIBCO	31095-029
EMEM No Phenol Red	GIBCO	51200-038
Fetal Bovine Serum	GIBCO	10270-106
Fetal Bovine Serum, charcoal stripped	GIBCO	12676029
0.5% Trypsin-EDTA 1x	GIBCO	25300-054
L-Glutamine 200 mM 100x	GIBCO	25030-024
Penicillin-Streptomycin	GIBCO	15140-122
Human Insulin (Humulin regular)	Lilly	U100
EGF	SIGMA	E-9644
Hydrocortisone	SIGMA	H-0888
Horse Serum	Life technologies	16050122
Cholera Toxin	SIGMA	C8052
Trizol Reagent	Ambion	15596018
Lipofectamine 3000	Invitrogen	11668-019
Proteinase K	ThermoFisher Scientific	AM2546
Protein G Plus / Protein A Agarose	Millipore	IP05
protease inhibitor cocktail, cOmplete EDTA-free	Roche	05 892 791 001
Na3VO4
MboI	New England BioLabs	r0147-mboi
Herculase II Fusion DNA Polymerase	Agilent	600675
AMPure XP beads	Beckman Coulter	A63881
Endopeptidase LysC,	Wako	125-05061
Sequencing grade Trypsin	Promega	V5111
Critical Commercial Assays
Ovation Ultralow DR Multiplex System 9-16 kit	NUGEN	0535-32
Micro BCA Protein Assay Kit	ThermoFisher Scientific	23235
qScript cDNA Synthesis kit	Quanta Biosciences	95047-025
LightCycler FastStart DNA Master SYBR Green I kit	Roche	03 515 885 001
Illumina TruSeq kit	Illumina	20020594
TruSeq Stranded Total RNA Library Prep Human/Mouse/Rat	Illumina	20020596
Pierce Coomassie (Bradford) kit	Thermo Fisher	23200
NEBNext DNA Library Prep Kit	New England BioLabs	NEB #E7645
Qubit HS kit	Thermo Fisher	Q32854
FISH Tag RNA Multicolor Kit	Thermo Fisher	mp32956
Gibson Assembly Master	New England Biolabs	E2611S
BsmbI	Thermo Fisher	ER0451
Anti-DYKDDDDK G1 Affinity Resin	Genscript	L00432
Anti-HA Agarose	Thermo Fisher Scientific	26181
NuPAGE MOPS SDS Running Buffer	Novex by Life Technology	NP0001
NuPAGE 4-12% Bis Tris Gels	Invitrogen	NP0335box
Skim Milk Powder	Sigma	70166-500G
XCell SureLock Mini-Cell Electrophoresis System	Thermo Fisher	EI0001
Deposited Data
ChIP-seq, RNA-seq, Hi-C data	This study	GSE120162
Human reference genome NCBI build 38, GRCh38	Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
CTCF ChIP-seq of T47D in -S	Le Dily et al., 2014	GSE53463
ChIP-seq of eGFP-ADNP in K562 cells	Consortium, 2012	GSE105573
ChIP-seq of mouse Adnp	Ostapcuk et al., 2018	GSE97945
Gene expression data of breast cancer samples	Ringnér et al., 2011	http://co.bmc.lu.se/gobo/
EP300 ChIP-seq in T98G	Ramos et al., 2010	GSE21026
Proteomic data: PRIDE	This study	PXD011250
Mendeley	This study	https://doi.org/10.17632/mzjf96t3gc.3
Experimental Models: Cell Lines
T47D	ATCC	CRL-2865
T98G	ATCC	CRL-1690
IMR90	ATCC	CCL-186
MCF10A	ATCC	CRL-10317
Oligonucleotides
UHRF1-associated AE H3K18ac ChIP Forward: ATTGTAAT CCCGGTCGTTTG	This study	NA
UHRF1-associated AE H3K18ac ChIP Reverse: CGGGTTC AAGTGATTCTCGT	This study	NA
UHRF1-expression Forward: GCCATACCCTCTTTCGACTACG	This study	NA
UHRF1-expression Reverse: GCCCCAATTCCGTCTCATCC	This study	NA
HELLS-associated AE H3K18ac ChIP:Forward: TAGCCTGGAATGGGCTAAT	This study	NA
HELLS-associated AE H3K18ac ChIP: Reverse: TCAGTTGATCCTCCCACCTC	This study	NA
PPIA primers: For – GCCGAGGAAAACCGTGTACT	This study	NA
PPIA primers: Rev- GTCTTTGGGACCTTGTCTGC	This study	NA
siGENOME against human GTF3C5 (9328) siRNA	Dharmacon	D-020031-02
siGENOME Non-Targeting siRNA Pool #2	Dharmacon	D-001206-14
siGENOME against human GTF3C1 siRNA	Dharmacon	LQ-012581-00-0002
siGENOME against human ADNP siRNA	Dharmacon	LQ-012857-01-0002
GTF3C5 expression Forward B: GCGGCAAGCATACGTCAATG	This study	NA
GTF3C5 expression Rev B: TGGTCGGTAGAAGTAGTCCAC	This study	NA
GAPDH expression forward: GACTCAACGGATTTGGTCGT	This study	NA
GAPDH expression reverse: TTGATTTTGGAGGGATCTCG	This study	NA
Oligo1 reverse: TGGGATTCCTGGATCCGGTGTTTCGTCCTTT CCACAAGAT	This study	NA
Oligo2 forward: CACCGGATCCAGGAATCCCACTTCTGTTTT AGAGCTAGAAGAGAC	This study	NA
Oligo3 reverse: GAGACGGGATCCTAGGAATTCCGTCTCTTC TAGCTCTAAAAC	This study	NA
Oligo4 forward: TTCCTAGGATCCCGTCTCTCTGTATGAGAC CACTCTTTCCC	This study	NA
Oligo5 reverse: AACAAACCAAAAAACCCCACAAAGGGAA AGAGTGGTCTCAT	This study	NA
Oligo6 forward: GGGGTTTTTTGGTTTGTTTTAGAGCTAGAA ATAGCAAGTT	This study	NA
C557F: GTTTTAGAGCTAGAAATAGCAAG	This study	NA
C557R: GTGGTCTCATACAGAACTTATAAG	This study	NA
C542F: GTACAAAATACGTGACGTAG	This study	NA
C542R: ATGTCTACTATTCTTTCCCC	This study	NA
gRNA1: GATCCAGGAATCCCACTTCT	This study	NA
gRNA2: TTTGTGGGGTTTTTTGGTTT	This study	NA
Alu_up3: CCGAAGGCTAAAAGCGACTA	This study	NA
Alu_down: ACGTTGGCAAGGATTTGAAG	This study	NA
GTF3C1_expression_for: GGGAAGCTGCACTATCACAGA	This study	NA
GTF3C1_expression_rev: GGTAATCGGATCACATGGGACT	This study	NA
ADNP_expression_for: CATGGGAGGATGTAGGACTGT	This study	NA
ADNP_expression_rev: ATGGACATTGCGGAAATGACT	This study	NA
Recombinant DNA
pDECKO_mCherry	Addgene	78534
pBIG2abc vector	Addgene	80617
Software and Algorithms
Samtools	Li et al., 2009	http://samtools.sourceforge.net/
FACS Diva Software v6.1.2	Becton Dickinson	NA
ModFit v3.2	Verity Software	NA
cis-egulatory annotation system (CEAS)	Shin et al., 2009	NA
Trimmomatic	Bolger et al., 2014	https://goo.gl/VzoqQq
STAR	Dobin et al., 2013	NA
ChIP-seq Enrich	Welch et al., 2014	http://chip-enrich.med.umich.edu/
DAVID	Dennis et al., 2003	https://david.ncifcrf.gov/
ImageJ	Rueden et al., 2017	https://imagej.nih.gov/ij
Xcalibur software v2.2	Thermo Fisher Scientific	OPTON-30487
Proteome Discoverer software suite v1.4	Thermo Fisher Scientific	OPTON-30812
Mascot search engine v2.5	Matrix Science	NA
SAINT software	Choi et al., 2011	http://saint-apms.sourceforge.net/Main.html
NucMap	Zhao et al., 2019	http://bigd.big.ac.cn/nucmap
Other
Gene expression analysis script	This paper	https://doi.org/10.17632/mzjf96t3gc.3
Hi-C analysis pipeline	Serra et al., 2017, Vidal et al., 2018