REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-ARID2 (E-3)	Santa Cruz	sc-166117; RRID: AB_2060382
Rabbit monoclonal anti-ATM (D2E2)	Cell Signaling Technology	2873; RRID: AB_2062659
Rabbit polyclonal anti-Baf180	Millipore	ABE70; RRID: AB_10807561
Rabbit polyclonal anti-BMI1	Bethyl Labs	A301-694A; RRID: AB_1210891
Mouse monoclonal anti-BRG1 (G7)	Santa Cruz	sc-17796; RRID: AB_626762
Rabbit polyclonal anti-CENPF	Bethyl Labs	A301-611A; RRID: AB_1210906
Rabbit polyclonal anti-CTCF	Millipore	07-729; RRID: AB_441965
Rabbit polyclonal anti-Cyclin D1	Neomarkers	RB-010-PO
Rabbit polyclonal anti-Esco2	Abcam	ab86003; RRID: AB_1924967
Rabbit monoclonal anti-EZH2	Cell Signaling Technology	5246; RRID: AB_10694683
Mouse monoclonal anti-GFP (B2)	Santa Cruz	sc-9996; RRID: AB_627695
Mouse monoclonal anti-H2A-K119ub (E5C5)	Millipore	05-678; RRID: AB_309899
Rat monoclonal anti-NIPBL	Abcam	ab106768; RRID: AB_10859516
Rabbit polyclonal anti-PDS5A	Abcam	ab122352; RRID: AB_11129705
Rabbit polyclonal anti-PDS5B	Abcam	ab70298; RRID: AB_1269710
Rabbit polyclonal anti-Rad21	Abcam	ab992; RRID: AB_2176601
Rabbit polyclonal anti-SMC3	Abcam	ab155587
Goat polyclonal anti-SA1	Abcam	ab4457; RRID: AB_2286589
Goat polyclonal anti-SA2	Abcam	ab4463; RRID: AB_304471
Rabbit polyclonal anti-WAPL	Abcam	ab70741; RRID: AB_2216719
Mouse monoclonal anti-α-tubulin	Abcam	ab7291; RRID: AB_2241126
Mouse monoclonal anti-γ-H2AX (pSer139) (JBW301)	Millipore	05-636; RRID: AB_309864
Goat Anti-Rabbit Immunoglobulins/HRP	Agilent (Dako)	P044801-2
Rabbit Anti-Mouse Immunoglobulins/HRP	Agilent (Dako)	P026002-2; RRID: AB_2636929
Rabbit Anti-Goat Immunoglobulins/HRP	Agilent (Dako)	P044901-2
Goat Anti-Rat Immunoglobulins/HRP	Millipore	AP136P; RRID: AB_91300
Goat Anti-Mouse IgG/FITC	Sigma-Aldrich	F0257-1ML
Sheep Anti-rabbit IgG/Cy3	Sigma-Aldrich	C2306-1ML
Goat Anti-Mouse IgG/Alexa Fluor 555	Thermo Fisher Scientific (Invitrogen)	A-21422; RRID: AB_141822
Chemicals, Peptides, and Recombinant Proteins
4-hydroxytamoxifen	Sigma-Aldrich	H7904-5MG
5,6-Dichlorobenzimidazole 1-β-D-ribofuranoside (DRB)	Sigma-Aldrich	D1916-10MG
ATM Kinase Inhibitor	Santa Cruz Biotechnology	sc-202963 (CAS 587871-26-9)
cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail	Sigma-Aldrich (Roche Applied Science)	04693159001
5α-Dihydrotestosterone (DHT)	Sigma-Aldrich	D-073-1ML
Doxycycline hyclate	Sigma-Aldrich	D9891-G
Hoechst 33258 solution	Sigma-Aldrich	94403-1ML
Propidium iodide	Thermo Fisher Scientific (Invitrogen)	P3566
RNase A	Sigma-Aldrich	R5503-100MG
Sheild1	Clontech Laboratories UK Ltd	632189
Thymidine	Sigma-Aldrich	T1895-5G
Critical Commercial Assays
Click-iT RNA Alexa Fluor 594 Imaging Kit	Thermo Fisher Scientific (Invitrogen)	C10330
HiPerFect Transfection Reagent	QIAGEN	301705
Lipofectamine RNAiMAX Transfection Reagent	Thermo Fisher Scientific (Invitrogen)	13778150
Lipofectamine LTX Reagent with PLUS Reagent	Thermo Fisher Scientific (Invitrogen)	15338100
Nucleospin Tissue	Machery-Nagel	740952.5
Power SYBR green PCR master mix	Thermo Fisher Scientific (Applied Biosystems)	4367659
Premo FUCCI Cell Cycle Sensor (BacMam 2.0)	Thermo Fisher Scientific (Invitrogen)	P36237
QIAGEN RNeasy Mini Kit	QIAGEN	74106
QuikChange II Site-Directed Mutagenesis Kit	Agilent	200523
SuperScript First-Strand Synthesis System for RT-PCR	Thermo Fisher Scientific (Invitrogen)	11904018
TurboFect Transfection Reagent	Thermo Fisher Scientific	R0531
TMPRSS2/ERG Deletion/Breakapart Probe	Cytocell	LPS 021
Deposited Data
Differential exome sequencing data and files	This paper	SAMN08226046
Human reference genome NCBI build 37, GRCh37	Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
Genomic data commons	Grossman, 2016	N/A
COSMIC database	Forbes et al., 2017	https://cancer.sanger.ac.uk
Raw data files deposited in Mendeley Data	This paper	https://doi.org/10.17632/4h486ty62f.1
Experimental Models: Cell Lines
U2OS	From cell line stocks at GDSC, Sussex University, validated by STR profiling with ECACC	N/A
U2OS 263 IFII	Gift from Roger Greenberg; Tang et al., 2013	N/A
U2OS 265	Gift from Roger Greenberg; Tang et al., 2013	N/A
LNCaP clone FGC	ATCC	CRL-1740
U2OS Baf180 KO CRISPR Clone 15	This paper	N/A
U2OS NTC sh	Hopkins et al., 2016	N/A
U2OS Baf180 sh	Hopkins et al., 2016	N/A
Oligonucleotides
siRNA sequence: ARID2 SMARTpool: ON-TARGETplus	Dharmacon	L-026945-01-0005
siRNA sequence: Baf180 SMARTpool: ON-TARGETplus	Dharmacon	L-008692-01-0005
siRNA sequence: BRG1 SMARTpool: ON-TARGETplus	Dharmacon	L-010431-00-0005
siRNA sequence: BRM SMARTpool: ON-TARGETplus	Dharmacon	L-017253-00-0005
siRNA sequence: CTCF SMARTpool: ON-TARGETplus	Dharmacon	L-020165-00-0005
siRNA sequence: Esco2 SMARTpool: ON-TARGETplus	Dharmacon	L-025788-01-0005
siRNA sequence: NIPBL SMARTpool: ON-TARGETplus	Dharmacon	L-012980-00-0005
siRNA sequence: NTC: Non-targeting pool: ON-TARGETplus	Dharmacon	D-001810-10-20
siRNA sequence: Rad21 SMARTpool: ON-TARGETplus	Dharmacon	L-006832-00-0005
siRNA sequence: SMC3 SMARTpool: ON-TARGETplus	Dharmacon	L-006834-00-0005
siRNA sequences for ATM, NTC, PDS5A, PDS5B, Sororin, STAG1, STAG2, WAPL, see Table S4	This paper	N/A
Primer: TMPRSS2_rtPCR FWD: CTGGTGGCTGATAGGGGAT	Lin et al., 2009	N/A
Primer: TMPRSS2_rtPCR REV: GTCTGCCCTCATTTGTCGAT	Lin et al., 2009	N/A
Primer: TMPRSS2-CR-3F: CACCGTTCATTCACGATCCCTAACA	Li et al., 2018	N/A
Primer: TMPRSS2-CR-3R: AAACTGTTAGGGATCGTGAATGAAC	Li et al., 2018	N/A
Primer: ERG-CR-2F: CACCGGGATGGTAAACGGAGAGTGC	Li et al., 2018	N/A
Primer: ERG-CR-2R: AAACGCACTCTCCGTTTACCATCCC	Li et al., 2018	N/A
Primer: TMPRSS2:ERG FWD: AGCGCGGCAGGAAGCCTTAT	Sigma	N/A
Primer: TMPRSS2:ERG REV: CCGTAGGCACACTCAAACAACGA	Mani, 2016	N/A
Primer: Reporter Transcript FWD: TCATTAGATCCTGAGAACTTCA	Shanbhag et al., 2010	N/A
Primer: Reporter Transcript REV: TTTTGGCAGAGGGAAAAAGA	Shanbhag et al., 2010	N/A
Primer: Actin_rtPCR FWD: GCTCGTCGTCGACAACGGCTC	Lin et al., 2009	N/A
Primer: Actin_rtPCR REV: CAAACATGATCTGGGTCATCTTCTC	Lin et al., 2009	N/A
Primer: cyclophilin A_rtPCR FWD: CTGGACCCAACACAAATGGT	This paper	N/A
Primer: cyclophilin A_rtPCR REV: GCCTTCTTTCACTTTGCCAAAC	This paper	N/A
Primer: Sororin_rtPCR FWD: AGTCTCGCCAGTGGTGTGCT	Zhang, 2011	N/A
Primer: Sororin_rtPCR REV: TTCAACCAGGAGATCAAACTGC	Zhang, 2011	N/A
Primer: GAPDH_rtPCR FWD: ACATCGCTCAGACACCATG	Meisenberg, 2015	N/A
Primer: GAPDH_rtPCR REV: TGTAGTTGAGGTCAATGAAGGG	Meisenberg, 2015	N/A
Primers for Site Directed Mutagenesis and creation of Rad21-pEGFP-C1 and STAG2-pmRFP-C1, see Table S4	This paper	N/A
Recombinant DNA
Plasmid: Baf180-pEGFP-C3	Kakarougkas et al., 2014	N/A
Plasmid: STAG2-pEGFP-C1	Solomon, 2011	Addgene plasmid: 31972
Plasmid: STAG2-pmRFP-C1	This paper	N/A
Plasmid: Rad21-pEGFP-C1	This paper	N/A
Plasmid: pEGFP-C1	Gift from Keith Caldecott (University of Sussex)	N/A
Plasmid: pmRFP-C1	Gift from Keith Caldecott (University of Sussex)	N/A
Plasmid: Cas9-gRNA	Horizon	free CRISPR guide program
pcDNA4-GFP-IRES-Puro	Gift from Keith Caldecott (University of Sussex)	N/A
pSpCas9(BB)-2A-Puro (PX459) V2.0	Gift from Helfrid Hochegger (University of Sussex)	N/A