Members of the L transposon family (long interspersed repeat DNA or LINE family) of rats are 6.7 kb long, 5 kb of which is devoted to protein encoding sequence (ORFs). A promoter-like sequence is at the left end of the element, and G-rich homopurine (GHP) stretches are at the other end. Although 5 kb or so of the rat and mouse L DNA is very highly conserved, their promoter-like sequences are completely distinct. This means that novel species-specific promoter sequences have been repeatedly acquired during the evolution of L families. The rat promoter sequence contains enough CpGs to qualify it as a """"""""CG island"""""""" and we have recently shown that this sequence functions as a promoter in vivo since it activates the prokaryotic chloramphenicol acyltransferase gene in rat cells. Furthermore, partial methylation of the promoter inhibits its activity by about 75% in these cells. All mammalian L elements contain at their right end GHP stretches. We recently showed that these sequences induce unpairing of contiguous duplex DNA such that this DNA can take up (hybridize) complementary DNA sequences. Furthermore, the hybridized DNA sequence can be elongated by added DNA polymerase. Both of these phenomena are essential intermediates in well-documented models for certain types of recombinational and transpositional events. This suggests that the L element GHP stretches may be very important for these properties of L DNA. Analysis of the structure of the GHP sequence itself, with a variety of chemical and enzymatic probes, showed that this sequence does not assume any stable non-B DNA basepaired structure, but rather exhibits significant single-stranded character. Therefore, the GHP stretch is functionally unpaired, and this property provides a straightforward explanation for the effect of GHP stretches on contiguous duplex DNA. Finally, we have identified a novel L DNA element in the rat genome that appears to be the ancestral L element from which both present day rat and mouse L families were derived. Study of this ancestral L element should clarify the evolutionary origin and fate of L DNA.
