An in vitro system has been developed to examine the influence of transcription on genetic rearrangement. Using a homologous pairing assay, the transfer of one strand of a nucleosomal template onto a recipient DNA molecule was monitored as a function of RNA polymerase activity. Transcriptionally inactive nucleosomal DNA was refractory to homologous pairing. Homologous pairing was catalyzed, however, by the eukaryotic recombinase, rec1, when the nucleosomal template was being transcribed. The reaction was found to be dependent on the presence of rec1, RNA polymerase, NTPs and RNA synthesis. Heteroduplex formation between a short DNA duplex fragment assembled into a nucleosome and a single-stranded circle relied also on the presence of sequence homology between the duplex and the circle. The results of this study lend support to the notion that transcriptionally active regions within a chromosome are more apt to serve as sites of genetic recombination.