<jats:title>Abstract</jats:title> <jats:p>The infinite variety of antigen-binding receptors originates from the rearrangement of B and T-cell receptor loci in a process known as V(D)J recombination. The initial site-specific DNA cleavage steps of this process are catalyzed by the lymphoid specific proteins RAG1 and RAG2. Deregulation of this process, leads to a spectrum of diseases including immunodeficiency and leukemia. These leukemias are believed to arise from RAG1/2 mediated oncogenic chromosomal translocations. The transcription factor Pax5 is critical for B cell development and is known that, it interacts with RAG1/2 and mediates V to DJ recombination. Pax5 is also been implicated in human B cell malignancies. Another multifunctional transcription factor, YY1, is known to play a role in V to DJ recombination similar to Pax5. We were able to see an interaction of YY1 with RAG1/2 and Pax5, when these proteins were over-expressed in 293T cells. When we performed a plasmid based recombination assay in presence of Pax5, YY1 or both a consistent decrease in recombination levels was observed. To elucidate the mechanism of inhibition, we analyzed the recombination intermediates and found that the initial cleavage step is inhibited by these two factors. In addition, purified Pax5 and YY1 inhibit the in vitro cleavage activity of RAG1/2 recombinase. The expression of a mutant Pax5 increased the RAG recombinase activity, suggesting the importance of these two factors in regulation of RAGs mediated recombination.</jats:p>