Appendix 1—key resources table.

Reagent type (species) or resource	Designation	Source or reference	Identifiers	Additional information
Cell line (H. sapiens)	OE19	ACACC	96071721
Cell line (H. sapiens)	CP-A	ATCC	KR-42421
Cell line (H. sapiens)	OE19-dCas9-KRAB	Rogerson et al., 2020		OE19 transfected with vector to express dCas9-KRAB under doxycycline control
Antibody	Rabbit monoclonal anti-Erk1/2 antibody	Cell Signalling Technology	4695S	(1:1000)
Antibody	Donkey polyclonal anti-mouse secondary antibody (800CW)	Licor	925–32,212	(1:10,000)
Antibody	Donkey polyclonal anti-rabbit secondary antibody (700CW)	Licor	925–32,213	(1:10,000)
Antibody	Mouse monoclonal anti-Cas9	Diagenode	C15200229	(1:10,000)
Antibody	Rabbit monoclonal anti-BRD4	Abcam	ab128874	0.5 µg/2–4 × 105 cells
Antibody	Rabbit polyclonal anti-CTCF	Merck-Millipore	07-729	0.5 µg/2–4 × 105 cells
Antibody	Rabbit polyclonal anti-H3K27ac	Abcam	ab4729	0.5 µg/2–4 × 105 cells
Antibody	Mouse polyclonal anti-H3K27me3	Merck-Millipore	07-449	0.5 µg/2–4 × 105 cells
Antibody	Rabbit polyclonal anti-H3K4me1	Abcam	ab8895	0.5 µg/2–4 × 105 cells
Antibody	Rabbit polyclonal anti-H3K4me2	Diagenode	pAb-035-010	0.5 µg/2–4 × 105 cells
Antibody	Rabbit poylclonal anti-H3K4me3	Abcam	ab8580	0.5 µg/2–4 × 105 cells
Antibody	Rabbit poylclonal anti-H3K36me3	Diagenode	pAb-058-010	0.5 µg/2–4 × 105 cells
Antibody	Mouse monoclonal anti-H4K20me1	Diagenode	mAb-147-010	0.5 µg/2–4 × 105 cells
Antibody	Mouse monoclonal anti-PolII	Abcam	ab817	0.5 µg/2–4 × 105 cells
Antibody	Rabbit polyclonal anti-PolII-S2	Abcam	ab5095	0.5 µg/2–4 × 105 cells
Antibody	Rabbit polyclonal anti-PolII-S5	Abcam	ab5131	0.5 µg/2–4 × 105 cells
Antibody	Rabbit polyclonal anti-Med1	https://www.antibodies.com/	A98044/10 UG	0.5 µg/2–4 × 105 cells
Recombinant DNA reagent	pGL3 reporter vector	Promega	E1761
Recombinant DNA reagent	hSTARR_ORI vector	Addgene	99296
Recombinant DNA reagent	pINDUCER20-GFP-AFOS	Britton et al., 2017		ADS5006
Recombinant DNA reagent	pCH110	Amersham
Recombinant DNA reagent	pMD2.G	Addgene	12259
Recombinant DNA reagent	psPAX2	Addgene	12260
Sequence-based reagent	Primers	This study		Primers for amplification through PCR (See supplementary file). Primers can be ordered through any commercial vendor.
Commercial assay or kit	Lipofectamine RNAiMAX	Thermo Fisher	13778150
Commercial assay or kit	Cell Line NucleofectorTM Kit V	Lonza	VCA-1003	Used on Amaxa Nucleofector II with program T-020
Commercial assay or kit	Dual-Light Luciferase & β-Galactosidase Reporter System	Thermo Fisher	T1003
Commercial assay or kit	SuperScript VILO Master Mix	Thermo Fisher	11755250
Commercial assay or kit	PureLink Genomic DNA Mini kit	Thermo Fisher	K182001
Commercial assay or kit	HiFi assemly	NEB	E5520S
Commercial assay or kit	QuantiTect SYBR Green RT-PCR Kit	Qiagen	204243
Commercial assay or kit	RNeasy Plus Mini Kit	Qiagen	74134
Commercial assay or kit	RNase-free DNase set	Qiagen	79254
Commercial assay or kit	Ampure XP beads	Beckman Coulter Agencourt	A63881
Commercial assay or kit	TruSeq stranded RNA library kit v2	Illumina	RS-122-2001
Commercial assay or kit	Nextera DNA library prep kit	Illumina	FC-121-1031
Commercial assay or kit	Nextera Index kit	Illumina	FC-121-1012
Commercial assay or kit	NEBNext high fidelity 2x PCR master mix	NEB	M0541
Commercial assay or kit	DNA Clean and Concentrator	Zymo	D4013
Commercial assay or kit	Polyfect	Qiagen	301107
Commercial assay or kit	PEG-it	System Biosciences	LV810A-1
Commercial assay or kit	Polybrene	EMD Millipore	TR-1003
Chemical compound, drug	Doxycycline	Sigma-Aldrich	D3447	Used at final concentration of 100 ng/ml
Chemical compound, drug	N3-kethoxal	Gift from Chuan He		Used at 5 mM
Peptide, recombinant protein	RNase	Sigma	R4642	Used at 100 μg/ml
Peptide, recombinant protein	pA-Tn5	Epicypher	15-1017
Peptide, recombinant protein	EGF	Thermo Fisher	10450-013	5 μg/l
Peptide, recombinant protein	Bovine pituitary extract	Thermo Fisher	1E+07	Used at 50 mg/l
Software, algorithm	Trimmomatic	Bolger et al., 2014	V0.34	http://www.usadellab.org/cms/?page=trimmomatic
Software, algorithm	ChromHMM	Ernst and Kellis, 2012
Software, algorithm	Bowtie2	Langmead and Salzberg, 2012	v2.3.0	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Software, algorithm	STAR	Dobin et al., 2013	V2.5.4	https://github.com/alexdobin/STAR
Software, algorithm	Macs2	Zhang et al., 2008	v2.1.1	https://github.com/taoliu/MACS
Software, algorithm	DEseq2	Love et al., 2014	V1.22.2	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Software, algorithm	TOBIAS	Bentsen et al., 2020	v0.5.1	https://github.com/loosolab/TOBIAS
Software, algorithm	featureCounts	Liao et al., 2014	V1.6.2	http://subread.sourceforge.net
Software, algorithm	FastQC		v0.11.4	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Software, algorithm	bedtools	Quinlan and Hall, 2010	v2.26.0	https://bedtools.readthedocs.io/en/latest/
Software, algorithm	DeepTools	Ramírez et al., 2016	V2.5.0	https://deeptools.readthedocs.io/en/develop/
Software, algorithm	Metascape	Zhou et al., 2019		https://metascape.org/gp/index.html
Software, algorithm	Homer	Heinz et al., 2010	v4.9	http://homer.ucsd.edu/homer/
Software, algorithm	R	R Development Core Team, 2018	v3.5.1	https://www.r-project.org/
Software, algorithm	GraphPad Prism		V8.0	https://www.graphpad.com/
Software, algorithm	Morpheus	Broad Institute		https://software.broadinstitute.org/morpheus/
Other	Crystal violet	Sigma-Aldrich	HT90132	Histological DNA stain. Used at concentration of 0.1%
Other	Gibco RPMI 1640	Thermo Fisher	52400	Cell culture medium for OE19s.
Other	Gibco fetal bovine serum	Thermo Fisher	10270	Cell culture supplement.
Other	Gibco penicillin/streptomycin	Thermo Fisher	15140122	Cell culture supplement
Other	Keratinocyte SFM (1×)	Thermo Fisher	17005042	Cell culture medium for CP-As.