Reagent/Resource	Reference or source	Identifier or catalog number
Experimental models
C57BL/6J (M. musculus)	Charles River	C57BL/6J
C57BL/6J (M. musculus) Nfil3−/−	van der Kallen et al (2015)	N/A
AML12 cells (M. musculus)	ATCC	CRL‐2254
HEK293 (H. sapiens)	ATCC	CRL‐1573
Recombinant DNA
pcDNA3.1‐mNFIL3	Addgene	Cat # 34572
pSGG5‐hHNF4A	Suaud et al (1999)	N/A
Antibodies
example: Rabbit‐anti‐H3	Abcam	Cat # ab1791
ACTB	Sigma‐Aldrich	Cat # A5441 (WB)
BRD4	Bethyl Labs	Cat # A301‐985A100 (ChIP)
BRD4	Wu et al (2006)	N/A (WB)
DDIT3	Santa Cruz	Cat # sc7351 (WB)
FOXA2	Abcam	Cat # ab23630 (WB, WES)
Histone H3	Cell Signaling	CST 3638S (WB)
H3K27ac	Active Motif	Cat # 39685 (ChIP)
HNF4A	Perseus	Cat # PP‐H1415‐00 (WB, WES)
LMNA	Santa Cruz	Cat # sc20681 (WB, WES)
NFIL3	Cell Signaling	Cat # CST 14312S (WB)
NR1H4	Perseus	Cat # PP‐A9033A‐00 (WB)
p‐Y416‐SRC	Cell Signaling	Cat # CST 6943S (WB)
SRC	Cell Signaling	Cat # CST 2109S (WB)
XBP1s	Cell Signaling	Cat # CST 12782S (WES)
TFIIB	Santa Cruz	Cat # sc7225 (WB)
EP300	Active motif	Cat #61401 (IP)
EP300	Santa Cruz	Cat # sc‐585 (WES)
IgG	Santa Cruz	Cat # sc‐2025 (IP)
HRP‐conjugated anti‐mouse	Sigma‐Aldrich	Cat # A4416 (WB)
HRP‐conjugated anti‐rabbit	Sigma‐Aldrich	Cat # A0545 (WB)
12–230 kDa Wes separation module	ProteinSimple	Cat# SM‐W004
66–440 kDa Jess or Wes Separation Module	ProteinSimple	Cat # SM‐W008
Oligonucleotides and sequence‐based reagents
qPCR primers	This study	Table EV5
Chemicals, enzymes and other reagents
example: T7 Endonuclease I	New England Biolabs	Cat # M03020S
Thapsigargin	Sigma‐Aldrich	Cat # T9033
Tunicamycin	Sigma‐Aldrich	Cat # T7765
MG132	Sigma‐Aldrich	Cat # M7449
PP2	Sigma‐Aldrich	Cat # P0042
Cycloheximide	Sigma‐Aldrich	Cat # C7698
JQ1	Sigma‐Aldrich	Cat # SML1524
Trichostatin A	Sigma‐Aldrich	Cat # T8552
C646	Sigma‐Aldrich	Cat # SML0002
MZ1	Tocris	Cat # 6154
TUDCA	Sigma‐Aldrich	Cat # T0266
PBA	Sigma‐Aldrich	Cat # SML0309
STF083010	Sigma‐Aldrich	Cat # SML0409
ISRIB	Sigma‐Aldrich	Cat # SML0843
AEBSF	Euromedex	Cat # 50985
jetPEI	Polyplus Transfection	Cat # 101‐40
High capacity cDNA reverse transciption kit	Applied Biosystems	Cat # 4368813
Brilliant II Sybr Green QPCR MAster mix	Agilent Biotechnologies	Cat # 600831
Disuccinimidyl glutarate (DSG)	Thermo Fischer Scientific	Cat # 20593
Formaldehyde	Sigma‐Aldrich	Cat# F8775
Benzonase	Sigma‐Aldrich	Cat# E1014
Protein A Sepharose	GE Healthcare	Cat # GE17‐1279‐01
Protein G Sepharose	GE Healthcare	Cat # GE17‐0618‐01
Complete protease inhibitor cocktail	Roche	Cat # 11836145001
Phosphatase inhibitor cocktail	Sigma‐Aldrich	Cat # P044
Proteinase K	Qiagen	Cat # 19133
tRNA	Sigma‐Aldrich	Cat # R5636
William's medium (MPH)	Lonza	Cat# BE12761F
DMEM/F12 (AML12)	Dutcher	Cat # P04‐41250
DMEM (HEK293)	Gibco‐Life Technologies	Cat #31966
Collagen	Roche	Cat# 11179179001
Collagenase	Sigma‐Aldrich	Cat # C5138
Yeast tRNA	Sigma‐Aldrich	Cat # R5636
Extract‐All (Trizol)	Eurobio	GEXEXT04‐0U
Software
Partek Genomics Suite 6.6	Partek	N/A
DESeq 1.26.0	Anders and Huber (2010)	N/A
FactoMineR 1.41	Lê et al (2008)	N/A
STEM v1.3.11	Ernst et al (2005)	N/A
GIANT	Vandel et al (2018)	N/A
Galaxy	Afgan et al (2018)	N/A
R	R Core Team (2015)	N/A
aplpack v1.3.2 R package	R Core Team (2015)	N/A
ToppGene Suite	Chen et al (2009)	N/A
GSEA v3.0	Subramanian et al (2005)	N/A
BubbleGUM v1.3.19	Spinelli et al (2015)	N/A
Bowtie 2	Langmead and Salzberg (2012)	N/A
Integrated Genome Browser (IGB 9.0.1)	Freese et al (2016)	N/A
MACS2	Chen et al (2015)	N/A
Rank Ordering of Super‐Enhancers (ROSE)	Loven et al (2013), Whyte et al (2013)	N/A
csaw v1.6.1	Lun and Smyth (2014, 2016)	N/A
Locus Overlap Analysis (LOLA 1.4.0)	Sheffield and Bock (2016)	N/A
gplots v3.0.1	Warnes et al (2016)	N/A
graphics R package	R Core Team (2015)	N/A
Prism v5 and 8	GraphPad	N/A
GeneSnap v7.12.06	Syngene	N/A
Image Studio Lite v5.2	LI‐COR Biosciences	N/A
Compass	ProteinSimple	N/A
bioDBnet	Mudunuri et al (2009)	N/A
Other
Influx sorter	Becton Dickinson	N/A
Agilent 2100 Bioanalyzer	Agilent Biotechnologies	N/A
MoGene‐2_0‐st	Affymetrix	N/A
GeneChip™ Scanner 3000 7G	Applied Biosystems	Cat# 00‐0210
GeneChip™ Fluidics Station 450	Applied Biosystems	Cat# 00‐0079
Bioruptor Pico	Diagenode	Cat# B01060010
MinElute PCR purification kit	Qiagen	Cat# 2800
ALT activity	Thermo Fischer Scientific	Cat# 981769
AST activity	Thermo Fischer Scientific	Cat# 981771
KONELAB 20	Thermo Fischer Scientific	Cat# 981801
Illumina Hi‐seq 4000	Illumina	N/A
G‐box	Syngene	N/A
Simple Western, WES system	ProteinSimple	N/A
TnT® Quick Coupled Transcription/Translation System	Promega	Cat# L5020
iBright™ CL1500 Imaging System	Thermo Fischer Scientific	A44240