Extended Data Table 2. Primers and siRNA used in this study.

NNN is the position of the optional index

Application	Name	Forward primer	Reverse primer
4C-seq	ViewpointDSB1	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTAACCTGGCAACTTATGAATCAGGA	CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTATGTCAAAAGCCAAGGGGACA
4C-seq	ViewpointDSB2	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTCCTTACGATTATTTGTGAATTTTG	CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGCTAATTCTGAGTTACATACATT
4C-seq	ViewpointDSB3	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTGATTACGTAGAAGGGTGCC	CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGGCAAATGATAACCCTGT
4C-seq	Viewpoint Ctrl region	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTCCTCAGGTTATCATCCCAA	CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCACCTTCGCTGTACCTTTG
4C-seq	Viewpoint CRISPR site	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTTAAGCACCCTCCTCCTAG	CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACCTTTACACCTCAAAACCT
4C-seq	Viewpoint470 kb upstream (Fig. 1c)	AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTACAAGGAAGAAGCAGGCATTCA	CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTTGAAATGAGTACTCTGCCATCCA
ChlP-qPCR	Ctrl region	AGCACATGGGATTTTGCAGG	TTCCCTCCTTTGTGTCACCA
ChlP-qPCR	DSB site 1	TCCCCTGTTTCTCAGCACTT	CTTCTGCTGTTCTGCGTCCT
ChlP-qPCR	DSB site 2	CCGCCAGAAAGTTTCCTAGA	CTCACCCTTGCAGCACTTG
ChlP-qPCR	DSB site 3	CCTAGCTGAGGTCGGTGCTA	GAAGAGTGAGGAGGGGGAGT
ChlP-qPCR	Cohesin positive site (mouse)	CAGAGATTTGCGGTGTTCGG	TTCACACCTAGAGGAGGGGT