Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes

Cell. 2015 Nov 5;163(4):947-59. doi: 10.1016/j.cell.2015.10.016. Epub 2015 Oct 22.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • CCCTC-Binding Factor
  • Chromosomes, Mammalian / chemistry
  • Chromosomes, Mammalian / metabolism*
  • DNA-Binding Proteins / metabolism
  • Genes, myc
  • Genome
  • High-Throughput Nucleotide Sequencing
  • Homeodomain Proteins / metabolism
  • Humans
  • Immunoglobulin Heavy Chains / genetics
  • Lymphoma / genetics
  • Mice
  • Nucleotide Motifs
  • Regulatory Sequences, Nucleic Acid*
  • Repressor Proteins / metabolism
  • Sequence Analysis, DNA
  • Translocation, Genetic
  • V(D)J Recombination*


  • CCCTC-Binding Factor
  • CTCF protein, human
  • Ctcf protein, mouse
  • DNA-Binding Proteins
  • Homeodomain Proteins
  • Immunoglobulin Heavy Chains
  • Rag2 protein, mouse
  • Repressor Proteins
  • RAG-1 protein

Associated data

  • GEO/GSE73007