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. Author manuscript; available in PMC: 2016 Nov 5.
Published in final edited form as: Cell. 2015 Oct 22;163(4):947–959. doi: 10.1016/j.cell.2015.10.016

Figure 3. DSBs Restricted in Genome-wide DEL-SJ-containing Loop Domains.

Figure 3

(A) Diagram showing major RAG-initiated joins in DEL-SJ-containing v-Abl pro-B cells. (B) Potential junctional outcomes between bait 12RSS and DSBs in cis include deletions, excision circles, and inversions. (C) Profiles of 12RSS junctions within chromosome X in ATM-deficient vAbl pro-B cells. Black triangles indicate insertion site of DEL-SJ. Junction numbers and percentages in + or − orientation upstream or downstream of bait 12RSS are shown separately. (D, E) Profiles of 23RSS junctions in the indicated 3.5-Mb region containing DEL-SJ on chromosome X. (F) ChIP-seq profiles of CTCF/Rad21 (upper panel) and heat map of in situ Hi-C (lower panel) in this 3.5-Mb region. (G–K) 12RSS and 23RSS junctions across the 1-Mb DEL-SJ-containing loop domain on chromosome 4. Stars indicate stronger cryptic RSSs. See also Figure S3 and Table S2.