Figure 3: Different chromatin loops are formed at the 3´-Tcra/Tcrd locus in DN3a and DP thymocytes. The V, D, and J gene segments are represented by black narrow rectangles. The Cδ and Cα regions are represented by black large rectangles. The diagram indicates the 5´- and the 3´-Trav/Trdv gene segments, the Trdd and Trdj gene segments, the Cδ region, the Trdv5 gene segment, the Traj gene segments, and the Cα region. The red lines indicate the areas occupied by 5´-Trav/Trdv , 3´-Trav/Trdv , Trdd and Trdj , and Traj gene segments. The position of the functionally relevant described regulatory elements is indicated as follows: INT1/2 as green circles, Eδ as a blue circle, TEAp as a purple circle, E3´-Jα as an orange circle, LCR as a pink line, Eα as a red circle, HS-1´as a black rectangle, and HS2-6 as brown ovals. Curved arrows represent the looping interactions between the regulatory elements demonstrated by 3C and 4C experiments [27,28]. In Rag-/- DN3a thymocytes, highfrequency looping interactions occur between the INT1/2 elements and the TEAp CTCF sites. In Rag-/- DP thymocytes, high frequency looping interactions occur between the Eα-, TEAp-, and the 3´-Trav/Trdv promoters-associated CTCF sites and bound TFs. These interactions are thought to promote the nucleation of recombination centers that facilitate both the Tcrd VDJ recombination in DN2/3a thymocytes and the Tcra VJ recombination in DP thymocytes involving distant gene segments.