We have previously reported that granulocyte-macrophage colony-stimulating factor (GM-CSF)- and interleukin-3 (IL-3)-dependent FDC-P1 cells undergo leukemic transformation when injected into sublethally irradiated DBA/2 mice. Transformation is related to aberrant activation of growth-regulatory genes by insertion of intracisternal A-particle (IAP) genomes. To elucidate the transformation process further, a subtracted cDNA library was constructed from a factor-independent leukemic FDC-P1 variant and the parental FDC-P1 cells. Screening for clones that were preferentially recognized by a total cDNA probe from the transformed cell line (in comparison to a similar probe from untransformed FDC-P1 cells) led to the isolation of 14 clones, of which six contained cDNA inserts encoding so-called B2 repeats, a class of short interspersed nucleotide elements. The expression of B2 repeats was significantly increased not only in the cell line from which the subtracted library was constructed, but also in all other leukemic FDC-P1 variants analyzed. B2 repeats can act as insertional mutagens and may have a role in the stabilization of certain oncogene and cytokine mRNAs. Interestingly, B2 repeats contain a 14-nucleotide region that is almost completely complementary to an AU-rich sequence in a region of the IAP mRNA encoding the enzyme reverse transcriptase. Although preliminary experiments to demonstrate stabilization of IAP mRNA by hybridization to B2 repeat sequences remained inconclusive, it is intriguing to speculate that B2 repeat sequences may have a causative role in the transformation process.