Possible alteration of genomic DNA in specific rat tissues

By employing in gel competitive reassociation, which distinguishes two DNA preparations, to clone anonymous DNA fragments with altered primary structure, we isolated a clone (BL-1) from a rat DNA which gave an extra, apparently altered, DNA band in a specific tissue (brain) when we used it as a probe for Southern hybridization. The sequence of BL-1 was very similar to a portion of LINE, a highly repetitive sequence. Southern hybridization analysis with oligonucleotide probes representing a portion of the BL-1 sequence confirmed the presence of the brain-specific band. Another, different band specific to HindIII digests of heart DNA was also detected with the same oligonucleotide probes. Furthermore, we found that poly (A) +RNA hybridized with BL-1 was enriched in brain. These results suggest that there are tissue specific alteration of genomic DNA in rats which may be associated with transcriptional activation specific to the sequence. Alternative explanations of the results are also discussed.