V(D)J recombination substrate choice is regulated to ensure that the appropriate gene segments are rearranged during lymphocyte development. It has been proposed that regulation of substrate usage is determined by changes in accessibility of the DNA targets. We show that Rag-mediated recombination of an episomal substrate in cells is affected by its packaging into chromatin. Chromatinized substrates were inefficiently rearranged, and methylation further reduced recombination. Disruption of nucleosomes by using butyrate on methylated substrates was sufficient to activate recombination, and dexamethasone could activate recombination in the absence of detectable transcription. Therefore, chromatin structure, and its manipulation by altering nucleosome positioning, can directly affect recombination efficiencies.Antigen receptor genes are assembled during lymphoid development from gene segments flanked by recombination signal sequences (RSSs) that are targets for the V(D)J recombination machinery (1). This nonhomologous site-specific recombination process must be precisely controlled because of the potentially severe consequences of aberrant chromosomal recombination events. Coexpression of the lymphoid-specific genes Rag-1 and Rag-2 occurs in developing B and T cells, ensuring that only the appropriate cell types are recombinationally active (2). A second level of regulation exists to control lineage specificity. Complete Ig gene rearrangement occurs only in B cells whereas T cell receptor genes rearrange exclusively in T cells (3). Moreover, within developing B and T cells, there are temporal controls over antigen receptor rearrangement. For example, in early B cells, the Ig heavy chain is rearranged before the light chain, and D to J H gene segments are