KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti- MD92-106	This Study	N/A
Anti- MD453-552	This Study	N/A
Anti-Pc	(Li et al., 2015)	N/A
Anti-EcR	Hybridoma bank	Cat#AB_528209; RRID:AB_528209
Anti-ISWI	Gift from John Tamkun	N/A
Deposited Data
MD92-106 ChIP-seq Kc167 Cells	This Study	GSE118047
MD453-552 ChIP-seq Kc167 Cells	This Study	GSE118047
MD92-106 20-HE ChIP-seq Kc167 Cells	This Study	GSE118047
MD453-552 20-HE ChIP-seq Kc167 Cells	This Study	GSE118047
ORGANIC Psq ChIP-seq S2 cells	(Kasinathan et al., 2014)	GSE45672
EcR ChIP-seq Kc167 Cells	This Study	GSE118047
EcR 20-HE ChIP-seq Kc167 Cells	This Study	GSE118047
MD453-552 HiChIP Kc167 Cells	This Study	GSE118047
MD453-552 20-HE HiChIP Kc167 Cells	This Study	GSE118047
Pc HiChIP Kc167 Cells	This Study	GSE118047
Pc 20-HE HiChIP Kc167 Cells	This Study	GSE118047
Pc ChIP-seq Kc167 Cells	This Study; (Li et al., 2015)	GSE118047; GSE63518
Pc 20-HE ChIP-seq Kc167 Cells	This Study	GSE118047
GAF ChIP-seq Kc167 Cells	(Cubeñas-Potts et al., 2017)	GSE80702
CBP ChIP-seq Kc167 Cells	(Li et al., 2015)	GSE63518
ISWI ChIP-seq Kc167 Cells	This Study	GSE118047
BEAF32 ChIP-seq Kc167 Cells	(Li et al., 2015; Yang et al., 2013)	GSE30740; GSE63518
CAPH2 ChIP-seq Kc167 Cells	(Li et al., 2015; Van Bortle et al., 2014)	GSE54529, GSE63518
Chromator ChIP-seq Kc167 Cells	(Li et al., 2015; Van Bortle et al., 2014)	GSE54529, GSE63518
CP190 ChIP-seq Kc167 Cells	(Van Bortle et al., 2014; Yang et al., 2013)	GSE30740, GSE54529
CTCF ChIP-seq Kc167 Cells	(Yang et al., 2013)	GSE30740
DREF ChIP-seq Kc167 Cells	(Li et al., 2015; Yang et al., 2013)	GSE63518, GSE39664
H3K27ac ChIP-seq Kc167 Cells	(Yang et al., 2013)	GSE36374
H3K27me3 ChIP-seq Kc167 Cells	(Rowley et al., 2017)	GSE89244
H3K4me1 ChIP-seq Kc167 Cells	(Li et al., 2015; Yang et al., 2013)	GSE36374, GSE63518
H3K4me3 ChIP-seq Kc167 Cells	(Li et al., 2015)	GSE63518
Hi-C Kc167 Cells	(Cubeñas-Potts et al., 2017)	GSE80702
L3mbt ChIP-seq Kc167 Cells	(Li et al., 2015; Van Bortle and Corces, 2013)	GSE36393, GSE63518
Mod(mdg4)2.2 ChIP-seq Kc167 Cells	(Van Bortle and Corces, 2013)	GSE36393
Nup98 ChIP-seq Kc167 Cells	(Cubeñas-Potts et al., 2017)	GSE80702
Rad21 ChIP-seq Kc167 Cells	(Li et al., 2015; Van Bortle et al., 2014)	GSE54529, GSE63518
Su(Hw) ChIP-seq Kc167 Cells	(Yang et al., 2013)	GSE30740
Z4 ChIP-seq Kc167 Cells	(Li et al., 2015)	GSE63518
STARR-seq	(Shlyueva et al., 2014; Zabidi et al., 2015)	GSE47691, GSE57876
Oligonucleotides
5′- CGACGGCAATTACATACCAG –3′	Psq-L&SFor	N/A
5′- GTTCGTGCTCGTGGTCCT-3′	Psq-L&S Rev	N/A
5′- CAACAGCAACAACACCCAGA –3′	Eip75B-RA For	N/A
5′- CAGATCGGCACATGGCTTT –3′	Eip75B-RA Rev	N/A
5′- GCACAGGCGCATTGTGATA –3′	Eip75B-RD For	N/A
5′- GGCGAAGAACTCCCGATATT –3′	Eip75B-RD Rev	N/A
5′- GATCCATAAGTCCGCAGTCAAA –3′	Vrille For	N/A
5′- CTATGGAGATGGAATGATGGCC –3′	Vrille Rev	N/A
5′- GCGGCCTATCTGTCTACTATTG –3′	CG44004 For	N/A
5′- ACGGAGCAATCTACGAAACC –3′	CG44004 Rev	N/A
Experimental Models: Cell Lines
D. melanogaster: Cell line Kc167	Drosophila Genomics Resource Center (DGRC)	FlyBase: FBtc0000001
Software and Algorithms
Juicebox	(Durand et al., 2016a)	http://aidenlab.org/juicebox/
Juicer	(Durand et al., 2016b)	http://aidenlab.org/juicer/
Chicago	(Cairns et al., 2016)	http://regulatorygenomicsgroup.org/chicago
ngsplot	(Shen et al., 2014)	https://github.com/shenlab-sinai/ngsplot
MANORM	(Shao et al., 2012)	http://bioinfo.sibs.ac.cn/shaolab/MAnorm/MAnorm.htm
Bowtie2	(Langmead et al., 2009)	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
MACS2	(Zhang et al., 2008)	https://github.com/taoliu/MACS