Sex-specific expression of alternative transcripts in Drosophila

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

Correlation of LEND and Diviner Data

Correlated results from the Lunar Reconnaissance Orbiter's (LRO) Lunar Exploration Neutron Detector (LEND) and Lunar Orbiting Laser Altimeter (LOLA) suggest insolation effects influence the spatial distribution of Lunar H poleward of 60deg latitude. Diviner results indicate an insolation induced thermal contrast between pole-facing and equator-facing slopes of crater walls. Our research shows that the contrasting thermal conditions observed in pole-facing vs equator-facing slopes and epithermal neutron rates from LEND are positively correlated. Numerical transformations of LOLA topography facilitated a systematic decomposition of LEND epithermal maps as a function of insolation effects. The results suggest a significantly positive local epithermal contrast in these regions. Comparing pole-facing and equator-facing slopes, we find that the pole-facing slopes show epithermal neutron suppression ranging from -0.005 to 0.02 cps relative to the equator-facing slopes .. We further investigate insolation effects on epithermal neutrons by comparing the predicted insolation contrast derived from the 3-D LOLA topography model with the LEND results. We also investigate and discuss the possibility of slope mass wasting effects being correlated with our insolation-effect hypothesi

SAS code

A Word file showing SAS-MAS code for the basic model and two different sets of Difference estimate

Raw Data

A .txt file containing all of the gene sequences used in probe design by Agilent, extracted from the Drosophila genome public release Version 3.0 (see http://www.fruitfly.org/sequence/release3genomic.shtml for latest version)

Supplementary Table 1

Expression and Classification Result

The Appalachian Writing Series from Bottom Dog Press

The poets from the Appalachian Writing Series of Bottom Dog Press will each read from their book of poetry including Marc Harshman, Jeanne Brynner, Karen Ktorba, Sandee Gertz Umbach, Hilda Downer. Introductions will be by coordinator and editor Larry Smith. This series, along with our fiction series, has kept the contemporary writing of Appalachia before the public. The poetry here has range and yet bears a common core in its insistence on understanding the culture and issues of the people of Appalachia. I would hope this presentation-performance could be given some prominence in the conference program. The press will be present at the book fair and in the conference publications

Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster.

Assessment of the degree to which gene expression is additive and heritable has important implications for understanding the maintenance of variation, adaptation, phenotypic divergence, and the mapping of genotype onto phenotype. We used whole-genome transcript profiling using Agilent long-oligonucleotide microarrays representing 12,017 genes to demonstrate that gene transcription is pervasively nonadditive in Drosophila melanogaster. Comparison of adults of two isogenic lines and their reciprocal F1 hybrids revealed 5820 genes as significantly different between at least two of the four genotypes in either males or females or across both sexes. Strikingly, while 25% of all genes differ between the two parents, 33% differ between both F1's and the parents, averaged across sexes. However, only 5% of genes show overdominance, suggesting that heterosis for expression is rare

Data from: Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster

Assessment of the degree to which gene expression is additive and heritable has important implications for understanding the maintenance of variation, adaptation, phenotypic divergence, and the mapping of genotype onto phenotype. We used whole-genome transcript profiling using Agilent long-oligonucleotide microarrays representing 12,017 genes to demonstrate that gene transcription is pervasively nonadditive in Drosophila melanogaster. Comparison of adults of two isogenic lines and their reciprocal F1 hybrids revealed 5820 genes as significantly different between at least two of the four genotypes in either males or females or across both sexes. Strikingly, while 25% of all genes differ between the two parents, 33% differ between both F1's and the parents, averaged across sexes. However, only 5% of genes show overdominance, suggesting that heterosis for expression is rare