MOUSE Y-SPECIFIC REPEATS ISOLATED BY WHOLE CHROMOSOME REPRESENTATIONAL DIFFERENCE ANALYSIS

Representational difference analysis (RDA) was used to generate Y-spec ific probes by enriching for and cloning the differences between the m ale (XY) and the female (XX) C57BL/6J mouse genomes. Characterization of 35 clones revealed 12 families related by sequence similarity, One clone from each family was chosen for detailed analysis by Southern bl ot hybridization, polymerase chain reaction (PCR) on normal and aberra nt genomes (Sxr), and fluorescence in situ hybridization. From one dif ference product we have characterized 12 Y-specific probes for hybridi zation, created seven male-specific PCR assays, mapped all repeat fami lies, and identified one repeat with a distinct XY homology. We report the first cloning of a Y-specific long interspersed repeat element (L INE) fragment. In total, RDA has identified six novel Y Chromosome rep eat families and allowed us to extend the characterization of six know n Y repeats. We conclude that this novel use of RDA for whole chromoso me subtraction successfully enriches chromosome-specific sequences and is suitable for the rapid generation of new Y Chromosome-specific pro bes. (C) 1996 Academic Press, Inc.