Mouse Y-specific repeats isolated by whole chromosome representational difference analysis.

A Navin; R Prekeris; N A Lisitsyn; M M Sonti; D A Grieco; S Narayanswami; E S Lander; E M Simpson

doi:10.1006/geno.1996.0473

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Mouse Y-specific repeats isolated by whole chromosome representational difference analysis.

A Navin·R Prekeris·N A Lisitsyn·M M Sonti·D A Grieco·S Narayanswami·E S Lander·E M Simpson

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Abstract

Representational difference analysis (RDA) was used to generate Y-specific probes by enriching for and cloning the differences between the male (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 blot hybridization, polymerase chain reaction (PCR) on normal and aberrant genomes (Sxr), and fluorescence in situ hybridization. From one difference product we have characterized 12 Y-specific probes for hybridization, created seven male-specific PCR assays, mapped all repeat families, and identified one repeat with a distinct XY homology. We report the first cloning of a Y-specific long interspersed repeat element (LINE) fragment. In total, RDA has identified six novel Y Chromosome repeat families and allowed us to extend the characterization of six known Y repeats. We conclude that this novel use of RDA for whole chromosome subtraction successfully enriches chromosome-specific sequences and is suitable for the rapid generation of new Y Chromosome-specific probes.

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Animals Base Sequence Blotting, Southern DNA Probes Female In Situ Hybridization, Fluorescence Male Mice Mice, Inbred C57BL Molecular Sequence Data Polymerase Chain Reaction Y Chromosome Journal Article Research Support, U.S. Gov't, Non-P.H.S.Research Support, U.S. Gov't, P.H.S.

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A Navin, R Prekeris, N A Lisitsyn, M M Sonti, D A Grieco, S Narayanswami, E S Lander, E M Simpson. 1996-09-01. Mouse Y-specific repeats isolated by whole chromosome representational difference analysis.. https://doi.org/10.1006/geno.1996.0473

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