Table 3. Antibodies used in this study.

Protein	Company	Catalogue No.	Species	Main Figure Reference
SA1	Abcam	ab4455	Mouse	1 a, c, d, e, 2 a, b, d, 3 a, b, c, d, e, g, h 4f,g, 5b, c, f, h, i
SA1	Abcam	ab4457	Mouse	1i
SA2	Bethyl	A300-159	Goat	1b, c, d, , 2 a, 3 a, b, c, f, 4 g, e, f, 5 c, d, e, f, g
SA2	Bethyl, AbVantage Pack	A310-941A	Goat	1i
CTCF	Diagenode	C15410210	Rabbit	1 c, d, i, 2 a
CTCF	Cell signalling	2899 s	Rabbit	1 a, e
RAD21	Abcam	ab992	Rabbit	1 c, d, i, 2 a, d, 4d, e, g, j
GFP-TRAP	ChromoTek	gtd-20		1i, 5f
GFP	Invitrogen	A11122	Rabbit	1 a, e
mAID	MBL	M214-3	Mouse	Figure 1—figure supplement 1a
OsTIR	MBL	PD048	Rabbit	Figure 1—figure supplement 1a
SMC3	Abcam	ab9263	Rabbit	1i
CHD6	Bethyl	A301-221A	Rabbit	2 a
MCM3	Bethyl	A300-124A	Goat	2 a, 3g, 5f
HNRNPUL2	Abcam	ab195338	Rabbit	2 a
YTHDC1	Abcam	ab122340	Rabbit	2d
FTSJ3	Bethyl	A304-199A-M	Rabbit	2d
FANCI	Bethyl	A301-254A-M	Rabbit	2d
TAF15	Abcam	ab134916	Rabbit	2d
DHX9	Abcam	Ab26271	Rabbit	2d
SSRP1	Abcam	ab26212	Mouse	2d
INO80	Proteintech	18810–1-AP	Rabbit	2d
ESYT2	Sigma-Aldrich	HPA002132	Rabbit	2d
S9.6	Kerafast	ENH001	Mouse	3d, g, h, 5f
RNASE H2	Novus	NBP1-76981	Rabbit	3g
AQR	Bethyl	A302-547A	Rabbit	3g, 5f, e
POLR2	Covance	MMS-1289	Mouse	3g
MAU2	Abcam	ab183033	Rabbit	4d, f
NIPBL	Abbiotec	250133	Rat	4d, f,
H3	Abcam	ab1791	Rabbit	4d, f, 5c
Name(SecondaryAbs)	Fluorophore	Company	Catalogue No.	Figure Reference
Donkey anti-Rabbit	Cy3_AF647	Home made from Jackson Immunoresearch IgG	Home made from 711-005-152	1e, Figure 1—figure supplement 1
Donkey anti-Goat	AF405_AF647	Home made from Jackson Immunoresearch IgG	Home made from 705-005-147	1e, Figure 1—figure supplement 1
Donkey anti-mouse	AF647	Invitrogen	A31570	1a, e, Figure 1—figure supplement 1b, e, Figure 3—figure supplement 1f
Donkey anti-rabbit	AF488	Invitrogen	A21206	1a, e, Figure 1—figure supplement 1b, e, Figure 3—figure supplement 1f
Donkey anti-rabbit	AF647	Invitrogen	A31573	1a, e, Figure 1—figure supplement 1b, e, Figure 3—figure supplement 1f
Donkey anti-goat	AF555	Invitrogen	A21432	1a, e, Figure 1—figure supplement 1b, e, Figure 3—figure supplement 1f
Donkey anti-goat	AF647	Invitrogen	A21447	1a, e, Figure 1—figure supplement 1b, e, Figure 3—figure supplement 1f
Goat anti-Mouse	AF568	ThermoFisher Scientific	A-11031	1a, e, Figure 1—figure supplement 1b, e, Figure 3—figure supplement 1f
Goat anti-Rabbit	AF647	ThermoFisher Scientific	A-21244	1a, e, Figure 1—figure supplement 1b, e, Figure 3—figure supplement 1f
Rabbit anti- Goat	AF647	ThermoFisher Scientific	A-21446