Three-way contact analysis characterizes the higher order organization of the Tcra locus

作者：Dai, Ranran; Zhu, Yongchang; Li, Zhaoqiang; Qin, Litao; Liu, Nan^*; Liao, Shixiu^*; Hao, Bingtao^*

来源：Nucleic Acids Research, 2023, 51(17): 8987-9000.

DOI：10.1093/nar/gkad641

• DOUBLE-STRANDED BREAKS
• GENE RECOMBINATION
• PRO-B
• ALPHA
• ENHANCER
• CTCF
• REARRANGEMENT
• DELTA
• ARCHITECTURE
• DELETION

The generation of highly diverse antigen receptors in T and B lymphocytes relies on V(D)J recombination. The enhancer E-& alpha; has been implicated in regulating the accessibility of V-& alpha; and J(& alpha;) genes through long-range interactions during rearrangements of the T-cell antigen receptor gene Tcra. However, direct evidence for E-& alpha; physically mediating the interaction of V-& alpha; and J(& alpha;) genes is still lacking. In this study, we utilized the 3C-HTGTS assay, a chromatin interaction technique based on 3C, to analyze the higher order chromatin structure of the Tcra locus. Our analysis revealed the presence of sufficient information in the 3C-HTGTS data to detect multiway contacts. Three-way contact analysis of the Tcra locus demonstrated the co-occurrence of the proximal J(& alpha;) genes, V-& alpha; genes and E-& alpha; in CD4(+)CD8(+) double-positive thymocytes. Notably, the INT2-TEAp loop emerged as a prominent structure likely to be responsible for bringing the proximal J(& alpha;) genes and the V-& alpha; genes into proximity. Moreover, the enhancer E-& alpha; utilizes this loop to establish physical proximity with the proximal V-& alpha; gene region. This study provides insights into the higher order chromatin structure of the Tcra locus, shedding light on the spatial organization of chromatin and its impact on V(D)J recombination.

• 单位
  郑州大学; 南方医科大学