Open Access Highly Accessed Research

Sex-specific expression of alternative transcripts in Drosophila

Lauren M McIntyre1*, Lisa M Bono2, Anne Genissel3, Rick Westerman24, Damion Junk25, Marina Telonis-Scott6, Larry Harshman7, Marta L Wayne6, Artyom Kopp34 and Sergey V Nuzhdin8

Author Affiliations

1 Department of Molecular Genetics and Microbiology, 1376 Mowry Road room 116, University of Florida, Gainesville, FL 32611, USA

2 Computational Genomics, 901 West State Street, Purdue University, West Lafayette, IN 47907, USA

3 Section of Evolution and Ecology, One Shields Avenue, University of California, Davis, California 95616, USA

4 Department of Horticulture, 625 Agriculture Mall Dr., Purdue University, West Lafayette, IN 47907, USA

5 Department of Agronomy, 915 West State Street, Purdue University, West Lafayette, IN 47907, USA

6 Department of Zoology, 223 Bartram Hall, University of Florida, Gainesville, FL 32611, USA

7 School of Biological Sciences, 335 Mant, University of Nebraska, Lincoln, NE 68588, USA

8 Center for Genetics and Development, One Shields Avenue, University of California, Davis, California, 95616, USA

For all author emails, please log on.

Genome Biology 2006, 7:R79  doi:10.1186/gb-2006-7-8-r79

Published: 25 August 2006

Abstract

Background

Many genes produce multiple transcripts due to alternative splicing or utilization of alternative transcription initiation/termination sites. This 'transcriptome expansion' is thought to increase phenotypic complexity by allowing a single locus to produce several functionally distinct proteins. However, sex, genetic and developmental variation in the representation of alternative transcripts has never been examined systematically. Here, we describe a genome-wide analysis of sex-specific expression of alternative transcripts in Drosophila melanogaster.

Results

We compared transcript profiles in males and females from eight Drosophila lines (OregonR and 2b, and 6 RIL) using a newly designed 60-mer oligonucleotide microarray that allows us to distinguish a large proportion of alternative transcripts. The new microarray incorporates 7,207 oligonucleotides, satisfying stringent binding and specificity criteria that target both the common and the unique regions of 2,768 multi-transcript genes, as well as 12,912 oligonucleotides that target genes with a single known transcript. We estimate that up to 22% of genes that produce multiple transcripts show a sex-specific bias in the representation of alternative transcripts. Sexual dimorphism in overall transcript abundance was evident for 53% of genes. The X chromosome contains a significantly higher proportion of genes with female-biased transcription than the autosomes. However, genes on the X chromosome are no more likely to have a sexual bias in alternative transcript representation than autosomal genes.

Conclusion

Widespread sex-specific expression of alternative transcripts in Drosophila suggests that a new level of sexual dimorphism at the molecular level exists.