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Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes

Hu, Jiazhi, Zhang, Yu, Zhao, Lijuan, Frock, Richard L., Du, Zhou, Meyers, Robin M., Meng, Fei-long, Schatz, David G., Alt, Frederick W.
Cell 2015 v.163 pp. 947-959
DNA damage, antibodies, antigens, chromatin, chromosome translocation, genes, loci, lymphocytes, signal peptide
RAG initiates antibody V(D)J recombination in developing lymphocytes by generating “on-target” DNA breaks at matched pairs of bona fide recombination signal sequences (RSSs). We employ bait RAG-generated breaks in endogenous or ectopically inserted RSS pairs to identify huge numbers of RAG “off-target” breaks. Such breaks occur at the simple CAC motif that defines the RSS cleavage site and are largely confined within convergent CTCF-binding element (CBE)-flanked loop domains containing bait RSS pairs. Marked orientation dependence of RAG off-target activity within loops spanning up to 2 megabases implies involvement of linear tracking. In this regard, major RAG off-targets in chromosomal translocations occur as convergent RSS pairs at enhancers within a loop. Finally, deletion of a CBE-based IgH locus element disrupts V(D)J recombination domains and, correspondingly, alters RAG on- and off-target distributions within IgH. Our findings reveal how RAG activity is developmentally focused and implicate mechanisms by which chromatin domains harness biological processes within them.