A new rat repetitive DNA family shows preferential localization on chromosome 3, 12 and Y after fluorescence in situ hybridization and contains a subfamily which is Y chromosome specific.

A DNA segment, containing a so far unknown repetitive DNA sequence has been isolated by reassociation of sheared total rat genomic DNA. FISH with this probe gave a strong hybridization signal on the satellites and in the centromeric region of chromosomes 3 and 12 and on the q-arm of the Y chromosome. A much weaker signal was seen in the centromeric region of chromosomes 11, 19 and X. The repeat unit of this repetitive DNA sequence is a 195-200 bp monomer, which is tandemly repeated. Screening of a rat genomic lambda library resulted in the isolation of variant members of this repeat family. FISH results with these members showed differences in their hybridization pattern especially when posthybridization washings were performed under higher stringency. Under these conditions one phage gave a strong hybridization signal only on the Y chromosome; other phage showed only weak hybridization patterns on different chromosomes. A subclone of the Y-specific phage was sequenced and showed large sequence homology with the 195-200 bp monomer. In Southern blot experiments this Y-specific sequence detects several male specific sequences, although some cross-hybridization with closely related sequences in both male and female DNA can also be observed.