All mammals contain several families of repetitive DNA sequences that comprise at least one-third of the genome. We have continued our characterization of the rat long, interspersed, repeated DNA family (or LINE family). This included determination of the DNA sequence of a full length (6.7 kb) member and of parts of several other members. Comparisons among these sequences and restriction enzyme analysis of the 40,000 or so genomic copies of the family showed that the sequenced 6.7 kb member is very typical of the family, both with respect to length and overall structure. Therefore, the rat LINE family is quite homogeneous, which is in marked contrast to the primate and mouse LINE families which are quite heterogeneous, and accounts for about 10% of the rat genome. Rat LINE members are highly transcribed, and their transcripts account for a substantial part of the nuclear RNA of various normal rat cells. Rat LINE members contain numerous long open reading frames, and potential regulatory sequences are present at both termini. Furthermore, the regulatory sequences in one of the termini strongly arrest DNA synthesis in vitro. This result is quite gratifying, since the presence of DNA arrest sites in chromosomal DNA has been surmised, but never demonstrated, and arrest sites have been implicated in some mechanisms for the amplification and transposition of mammalian DNA sequences. By using deleted and base substituted versions of these arrest site sequences, we have established the biochemical requirements for DNA arrest in vitro and are now examining the properties of these sites in vivo. DNA sequence analysis showed that several chromosomal target sites at which full length members have inserted, although not homologous overall, share a structural motif that clearly defines a class of target sites. Since LINE insertion is due to an illegitimate recombinational event and since such events underly many important normal and pathological genetic rearrangements in mammalian genomes, these results are quite provocative, especially in light of the paucity of information on what governs illegitimate recombination.
