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Nucleic Acids Research Advance Access published online on December 8, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl919
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© 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis

Donglin Liu1, J. Michael Brockman1,2, Brinda Dass3, Lucie N. Hutchins1, Priyam Singh1,2, John R. McCarrey4, Clinton C. MacDonald3 and Joel H. Graber1,2,*

1 The Jackson Laboratory, 600 Main Street Bar Harbor, ME 04609, USA 2 Bioinformatics Program, Boston University 24 Cummington Street, Boston, MA 02215, USA 3 Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center Lubbock, TX 79430, USA 4 Department of Biology, University of Texas at San Antonio San Antonio, TX 78249, USA

*To whom correspondence should be addressed. Tel: +1 207 288 6847; Fax: +1 207 288 6073; Email: joel.graber{at}jax.org

Received June 23, 2006. Revised September 29, 2006. Accepted October 17, 2006.

Gene expression and processing during mouse male germ cell maturation (spermatogenesis) is highly specialized. Previous reports have suggested that there is a high incidence of alternative 3'-processing in male germ cell mRNAs, including reduced usage of the canonical polyadenylation signal, AAUAAA. We used EST libraries generated from mouse testicular cells to identify 3'-processing sites used at various stages of spermatogenesis (spermatogonia, spermatocytes and round spermatids) and testicular somatic Sertoli cells. We assessed differences in 3'-processing characteristics in the testicular samples, compared to control sets of widely used 3'-processing sites. Using a new method for comparison of degenerate regulatory elements between sequence samples, we identified significant changes in the use of putative 3'-processing regulatory sequence elements in all spermatogenic cell types. In addition, we observed a trend towards truncated 3'-untranslated regions (3'-UTRs), with the most significant differences apparent in round spermatids. In contrast, Sertoli cells displayed a much smaller trend towards 3'-UTR truncation and no significant difference in 3'-processing regulatory sequences. Finally, we identified a number of genes encoding mRNAs that were specifically subject to alternative 3'-processing during meiosis and postmeiotic development. Our results highlight developmental differences in polyadenylation site choice and in the elements that likely control them during spermatogenesis.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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