Open Access Research

Identification of novel Y chromosome encoded transcripts by testis transcriptome analysis of mice with deletions of the Y chromosome long arm

Aminata Touré1, Emily J Clemente2, Peter JI Ellis2, Shantha K Mahadevaiah1, Obah A Ojarikre1, Penny AF Ball3, Louise Reynard1, Kate L Loveland3, Paul S Burgoyne1* and Nabeel A Affara2

Author Affiliations

1 Division of Developmental Genetics, MRC National Institute for Medical Research, Mill Hill, London, NW7 1AA, UK

2 University of Cambridge, Department of Pathology, Tennis Court Road, Cambridge, CB2 1QP, UK

3 Monash Institute of Medical Research, Monash University, and The Australian Research Council Centre of Excellence in Biotechnology and Development, Melbourne, Victoria 3168 Australia

For all author emails, please log on.

Genome Biology 2005, 6:R102  doi:10.1186/gb-2005-6-12-r102

Published: 2 December 2005

Abstract

Background

The male-specific region of the mouse Y chromosome long arm (MSYq) is comprised largely of repeated DNA, including multiple copies of the spermatid-expressed Ssty gene family. Large deletions of MSYq are associated with sperm head defects for which Ssty deficiency has been presumed to be responsible.

Results

In a search for further candidate genes associated with these defects we analyzed changes in the testis transcriptome resulting from MSYq deletions, using testis cDNA microarrays. This approach, aided by accumulating mouse MSYq sequence information, identified transcripts derived from two further spermatid-expressed multicopy MSYq gene families; like Ssty, each of these new MSYq gene families has multicopy relatives on the X chromosome. The Sly family encodes a protein with homology to the chromatin-associated proteins XLR and XMR that are encoded by the X chromosomal relatives. The second MSYq gene family was identified because the transcripts hybridized to a microarrayed X chromosome-encoded testis cDNA. The X loci ('Astx') encoding this cDNA had 92-94% sequence identity to over 100 putative Y loci ('Asty') across exons and introns; only low level Asty transcription was detected. More strongly transcribed recombinant loci were identified that included Asty exons 2-4 preceded by Ssty1 exons 1, 2 and part of exon 3. Transcription from the Ssty1 promotor generated spermatid-specific transcripts that, in addition to the variable inclusion of Ssty1 and Asty exons, included additional exons because of the serendipitous presence of splice sites further downstream.

Conclusion

We identified further MSYq-encoded transcripts expressed in spermatids and deriving from multicopy Y genes, deficiency of which may underlie the defects in sperm development associated with MSYq deletions.