Tcra gene recombination is supported by a Tcra enhancer- and CTCF-dependent chromatin hub

Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):E3493-502. doi: 10.1073/pnas.1214131109. Epub 2012 Nov 19.


Antigen receptor locus V(D)J recombination requires interactions between widely separated variable (V), diversity (D), and joining (J) gene segments, but the mechanisms that generate these interactions are not well understood. Here we assessed mechanisms that direct developmental stage-specific long-distance interactions at the Tcra/Tcrd locus. The Tcra/Tcrd locus recombines Tcrd gene segments in CD4(-)CD8(-) double-negative thymocytes and Tcra gene segments in CD4(+)CD8(+) double-positive thymocytes. Initial V(α)-to-J(α) recombination occurs within a chromosomal domain that displays a contracted conformation in both thymocyte subsets. We used chromosome conformation capture to demonstrate that the Tcra enhancer (E(α)) interacts directly with V(α) and J(α) gene segments distributed across this domain, specifically in double-positive thymocytes. Moreover, E(α) promotes interactions between these V(α) and J(α) segments that should facilitate their synapsis. We found that the CCCTC-binding factor (CTCF) binds to E(α) and to many locus promoters, biases E(α) to interact with these promoters, and is required for efficient V(α)-J(α) recombination. Our data indicate that E(α) and CTCF cooperate to create a developmentally regulated chromatin hub that supports V(α)-J(α) synapsis and recombination.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Base Sequence
  • CCCTC-Binding Factor
  • Chromatin / genetics*
  • Chromatin / immunology*
  • DNA Primers / genetics
  • Enhancer Elements, Genetic
  • Genes, T-Cell Receptor alpha*
  • Genes, T-Cell Receptor delta
  • Mice
  • Mice, 129 Strain
  • Mice, Inbred C57BL
  • Mice, Knockout
  • Mice, Transgenic
  • Models, Genetic
  • Models, Immunological
  • Repressor Proteins / genetics*
  • T-Lymphocytes / immunology
  • V(D)J Recombination*


  • CCCTC-Binding Factor
  • Chromatin
  • Ctcf protein, mouse
  • DNA Primers
  • Repressor Proteins

Associated data

  • GEO/GSE41743