Extended Data Fig. 6: RAG targeting and transcriptional activity analysis in the DFL16.1JH4-inv lines.
From: The fundamental role of chromatin loop extrusion in physiological V(D)J recombination
a, Generation of the DFL16.1JH4-inv line. Schematic shows two Igh alleles of DFL16.1JH4 line and DFL16.1JH4-inv line. In the DFL16.1JH4 line, one Igh allele contains a nonproductive VDJ join involving VH1-2P and JH3, and the other allele harbours the DFL16.1JH4 join. The DFL16.1JH4-inv line was derived from the DFL16.1JH4 line by inverting a 1-kb segment encompassing the DJH join using CRISPR–Cas9. b, Illustration of mechanism for RAG cryptic scanning activity from the RC DJH-RSS in DFL16.1JH4 line (top), DFL16.1JH4-inv line (middle) and DFL16.1JH4-inv 3′ CBEs−/− line (bottom). c, Representative HTGTS V(D)J-seq profiles showing RAG cryptic scanning patterns of DFL16.1JH4 line (top; n = 3 technical repeats), DFL16.1JH4-inv line (middle; n = 3 biological replicates) and DFL16.1JH4-inv 3′ CBEs−/− line (bottom; n = 3 biological replicates). Black line indicates bait primer position. Yellow shadows highlight RAG scanning regions. Purple arrows underneath the RAG targeting profiles indicate positions of forward and reverse CBEs. d, Representative GRO-seq profile of three repeats of the DFL16.1JH4-inv Rag2−/− line (n = 3 biological replicates).
