title: Sex-specific expression of alternative transcripts in Drosophila.
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.
  
  
  CONCLUSIONS
  Widespread sex-specific expression of alternative transcripts in Drosophila suggests that a new level of sexual dimorphism at the molecular level exists.
authors.affiliation: Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32611, USA. mcintyre@ufl.edu
authors.forename: Lauren M
authors.initials: LM
authors.lastname: McIntyre
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Bono
authors.forename: Anne
authors.initials: A
authors.lastname: Genissel
authors.forename: Rick
authors.initials: R
authors.lastname: Westerman
authors.forename: Damion
authors.initials: D
authors.lastname: Junk
authors.forename: Marina
authors.initials: M
authors.lastname: Telonis-Scott
authors.forename: Larry
authors.initials: L
authors.lastname: Harshman
authors.forename: Marta L
authors.initials: ML
authors.lastname: Wayne
authors.forename: Artyom
authors.initials: A
authors.lastname: Kopp
authors.forename: Sergey V
authors.initials: SV
authors.lastname: Nuzhdin
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D000704:Analysis of Variance; D000818:Animals; D004331:Drosophila melanogaster / Q000235:genetics* / Q000378:metabolism; D005260:Female; D015870:Gene Expression; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods*; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D012727:Sex Characteristics