Research

Sex-specific expression of alternative transcripts in Drosophila

Lauren M McIntyre¹ , Lisa M Bono² , Anne Genissel³ , Rick Westerman^2,4 , Damion Junk^2,5 , Marina Telonis-Scott⁶ , Larry Harshman⁷ , Marta L Wayne⁶ , Artyom Kopp^3,4 and Sergey V Nuzhdin⁸

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

author email corresponding author email

Genome Biology 2006, 7:R79doi:10.1186/gb-2006-7-8-r79

Published:	25 August 2006

Subject areas: Genome studies, Molecular biology

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.