Figure 2.
The proximal Vα genes, the proximal Jα genes and Eα form a chromatin hub in DP thymocytes. (A) Schematic diagram illustrating the linear structure of the Tcrα–Tcrd locus and its cis-regulatory elements. Eα and Eδ are enhancers of the Tcra and Tcrd genes, respectively. TEAp is the upstream promoter of the Jα gene array. EACBE is the CTCF-binding site located immediately downstream of Eα. (B) ChIP-seq profiles of CTCF, Rad21 and Nipbl are depicted on the top. Genome browser tracks below display chromatin interactions of the second–third fragments in the 3′ portion of the Tcra–Tcrd locus from the bait of Eα, TEAp, Trav17 or INT2. The red arrows highlight the baits on the top. Strong interactions are observed between INTs and Eα, as well as between the proximal Vα and Jα genes. Representative tracks for loops are shown from one of three independent experiments. Resolution: 5 kb; coordinates (mm10): chr14:53700000–54300000. (C) Comparison of read counts for Eα–TEAp–Trav17 (left) or Eα–TEAp–Trav21 (right) triplets and the proportions of these triplets relative to all pairwise interactions. Bar graphs represent the average normalized unique read counts in three replicates, with individual data points overlaid as dot plots. (D–G) Heatmaps showing three-way contacts of the 3′ portion of the Tcra–Tcrd locus from the bait of (D) Eα, (E) TEAp, (F) Trav17 or (G) INT2. The red arrow highlights the bait position. Each point represents the mean number of normalized unique interactions per restriction fragment in three replicates. Resolution: 5 kb; coordinates (mm10): chr14:53740000–54300000.