All metazoans examined to date contain families of repetitive DNA sequences which in mammals account for about 30% of the genome. In the past year we completed an extensive characterization of the rat long, interspersed, repeated DNA family (or LINE family) which included determination of the DNA sequence of a full length (6.7 kb) member and of parts of two 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 transcribed in largely an asymmetric way, and their transcripts account for a substantial part of the nuclear RNA of various normal rat cells. Rat LINE members contain long open reading frames (800-1900 bp, depending on the member), and a potential transcription start site is present at one end. The other end of the LINE sequence strongly arrests DNA synthesis in vitro, a result that 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. DNA sequence analysis showed that three 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.
