Highly repeated DNA families in the rat

We have analyzed the repeated DNA fraction of the rat by characterizing approximately 500 repeat DNA-containing clones using hybridization to a variety of rodent nucleic acids. To facilitate this analysis we devised a method whereby the cloned DNA is transferred to nitrocellulose paper by blotting directly out of colonies of the bacterial clones. In addition to identifying repeated sequences of potential interest (e.g. those transcribed in a tissue-specific manner, or those that are highly conserved in non-rat genomes), we found that, in contrast to what is revealed by the reassociation of rat DNA (e.g. Pearson, W. R., Wu, J. R., and Bonner, J. (1978) Biochemistry 17, 51-59), the rat genome contains a number of different highly repeated (greater than 50,000 copies) sequences. We distinguished the different highly repeated sequences both by their hybridization to different nucleic acids as well as by DNA sequence determination. The highly repeated sequences shared three characteristics that distinguished each of them from the 100,000-member rat satellite I family: (i) they were recovered less often in the cloned repeat DNA library than expected from their copy number in the rat genome; (ii) they reannealed abnormally slowly for their copy number even though they are not significantly divergent; and (iii) they are transcribed in one or more rat tissues. The implications of these findings for the organization of repeated sequences in the rat genome are discussed.