KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti- RNAPII	Biolegend	Cat# 664906; RRID:AB_2565554
Anti- Rad21	Schaaf et al., 2013	N/A
Anti-Cap-H2	Li etal., 2015	N/A
Anti-Slimb	Brownlee et al., 2011	N/A
Deposited Data
CTL Hi-C	Cubeñas-Potts et al., 2017	GSE80702
FLV Hi-C	This study; Li et al., 2015	GSE63518
Rad21 KD Hi-C	Li etal., 2015	GSE63518
Cap-H2 KD Hi-C	Li etal., 2015	GSE63518
Slimb KD Hi-C	This study	GSE118756
RNAPII HiChIP	This study	GSE118756
RNAPII ChIA-PET	Rowley et al., 2017	GSE89244
Rad21 HiChIP	This study	GSE118756
S2 Hi-C	Wang et al., 2018	GSE101317
ATAC-seq	Rowley et al., 2017	GSE89244
CTL Rad21 ChIP-seq	This study; Li et al., 2015; Van Bortle et al., 2014	GSE54529; GSE63518
FLV Rad21 ChIP-seq	This study	GSE118756
CTL Cap-H2 ChIP-seq	This study; Li et al., 2015; Van Bortle et al., 2014	GSE54529; GSE63518
FLV Cap-H2 ChIP-seq	This study	GSE118756
CTL RNAPII ChIP-seq	This study; Li et al., 2015	GSE63518
FLV RNAPII ChIP-seq FLV	Li etal., 2015	GSE63518
RNAPII ChIP-seq Rad21 KD	This study	GSE118756
RNAPII ChIP-seq Cap-H2 KD	This study	GSE118756
RNAPIISer2ph ChIP-seq in mouse sperm	Yoon Hee Jung personal communication	GSE116857
APBS ChIP-seq Datasets	Cubeñas-Potts et al., 2017; Li et al., 2015; Van Bortle et al., 2014; Yang et al., 2013	GSE30740;
		GSE63518;
		GSE54529,
		GSE80702
Hi-C mouse sperm	Jung et al., 2017	GSE79230
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
Bowtie2	Langmead et al., 2009	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
MACS2	Zhang et al., 2008	https://github.com/taoliu/MACS
MAnorm	Shao et al., 2012	http://bcb.dfci.harvard.edu/~gcyuan/MAnorm/MAnorm.htm