During the recombination of variable (V) and joining (J) gene segments at the T cell receptor ␣ locus, a V␣J␣ joint resulting from primary rearrangement can be replaced by subsequent rounds of secondary rearrangement that use progressively more 5 V␣ segments and progressively more 3 J␣ segments. To understand the mechanisms that target secondary T cell receptor ␣ recombination, we studied the behavior of a T cell receptor ␣ allele (HY␣) engineered to mimic a natural primary rearrangement of TRAV17 to J␣57. The introduced V␣J␣ segment was shown to provide chromatin accessibility to J␣ segments situated within several kilobases downstream and to suppress germ-line J␣ promoter activity and accessibility at greater distances. As a consequence, the V␣J␣ segment directed secondary recombination events to a subset of J␣ segments immediately downstream from the primary rearrangement. The data provide the mechanistic basis for a model of primary and secondary T cell receptor ␣ recombination in which recombination events progress in multiple small steps down the J␣ array. Expression of a functional T cell receptor (TCR) protein leads to the development of CD4 ϩ CD8 ϩ double-positive (DP) thymocytes, which then rearrange the Tcra locus (2). Tcra locus rearrangement is unique in several respects. First, primary Tcra rearrangements use J␣ segments at the 5Ј end of the 65-kb J␣ array (3-6). Second, primary rearrangements can be replaced by secondary rearrangements that use progressively more 3Ј J␣ segments until a selectable ␣ TCR is generated (7-12). Third, rearrangement occurs on both alleles in a relatively synchronous manner without allelic exclusion (10,13,14). Rearrangement terminates by down-regulation of recombinase expression as a result of positive selection or by apoptosis if positive selection fails to occur (6,(15)(16)(17). Positive selection allows the development of CD4 ϩ CD8 Ϫ or CD4 Ϫ CD8 ϩ single-positive thymocytes, which then exit the thymus to the circulation. Although much is known about primary rearrangements, little is known about the mechanisms that control secondary rearrangements.Multiple regulatory elements are known to activate and control accessibility to the J␣ array (composed of 61 J␣ segments) in DP thymocytes. The Tcra enhancer (E␣) at the 3Ј end of the Tcra locus was shown by gene targeting to control all V␣-to-J␣ rearrangements and to maintain the J␣ array in an accessible state in DP thymocytes (18,19). However, E␣-dependent accessibility also requires the activation of germ-line promoters within the J␣ array. The T early ␣ (TEA) and J␣49 promoters were identified at the 5Ј end of the J␣ array and were shown to account for the majority of primary rearrangements (20,21). Rearrangements in mice lacking both promoters were substantially reduced across the entire 5Ј region, recovering to normal levels by J␣37 (21). Two models have been proposed to explain the targeting of primary and secondary rearrangements (6,13,20). The ''developmental windows'' model suggests that sequential activation o...