Transcriptional measurements of mouse repeated DNA sequences

We have carried out transcriptional measurements on several families of repeated sequences to define their expression in mouse cells. The majority of Alu family transcripts result from read-through from adjacent structural gene promoters while 20% are discrete RNA polymerase III products. Alu repeat members show preferential orientation within RNA polymerase II transcription units as evidenced by asymmetric representation of the complementary strands of the Alu family in hnRNA. We assessed whether 3 non-Alu repeated sequence families had their own promoters by strand symmetry measurements and size distribution analysis of repeat-homologous newly synthesized nuclear RNA. Transcription homologous to the R family is totally symmetric and is likely due to read-through from adjacent structural gene promoters. LLRep1 and Bam5 repeats, in contrast, exhibit consistent strand asymmetry which is suggestive that at least some members may be transcribed by their own promoters. Among 3 mouse tissues and 1 cultured cell line analyzed, no quantitative variation in the expression of any of these sequences was observed.