Constraint and turnover in sex-biased gene expression in the genus Drosophila

Zhang, Yu; Sturgill, David; Parisi, Michael; Kumar, Sudhir; Oliver, Brian

doi:10.1038/nature06323

Cited by 280 publications

(455 citation statements)

References 39 publications

(32 reference statements)

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“…Overall, the expression profiles were similar to one another, with Spearman correlation coefficients of species pairs ranging between 0.68 and 0.90. Our expression data were also consistent with the previous studies of gene expression across multiple Drosophila species (Chen et al., 2014; Zhang, Sturgill, Parisi, Kumar & Oliver, 2007; Figure S2a).…”

Section: Resultsmentioning

confidence: 99%

“…We compared our expression data with two previous studies of gene expression across multiple Drosophila species (Chen et al., 2014; Zhang et al., 2007)—GSE99574 is based on RNA‐seq and GSE6640 is based on microarrays (herein referred to as “reference studies”). For simplicity, we used only “male replicate 1” in each reference study for whole‐body expression.…”

Section: Methodsmentioning

confidence: 99%

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Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

Avanesov

Porter

et al. 2018

Aging Cell

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SummaryLifespan varies dramatically among species, but the biological basis is not well understood. Previous studies in model organisms revealed the importance of nutrient sensing, mTOR, NAD/sirtuins, and insulin/IGF1 signaling in lifespan control. By studying life‐history traits and transcriptomes of 14 Drosophila species differing more than sixfold in lifespan, we explored expression divergence and identified genes and processes that correlate with longevity. These longevity signatures suggested that longer‐lived flies upregulate fatty acid metabolism, downregulate neuronal system development and activin signaling, and alter dynamics of RNA splicing. Interestingly, these gene expression patterns resembled those of flies under dietary restriction and several other lifespan‐extending interventions, although on the individual gene level, there was no significant overlap with genes previously reported to have lifespan‐extension effects. We experimentally tested the lifespan regulation potential of several candidate genes and found no consistent effects, suggesting that individual genes generally do not explain the observed longevity patterns. Instead, it appears that lifespan regulation across species is modulated by complex relationships at the system level represented by global gene expression.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

Avanesov

Porter

et al. 2018

Aging Cell

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“…Not surprisingly, female and male gonads usually differ remarkably in the sets of highly expressed genes [4][5][6][7]. Sex-biased gene expression, although less pronounced than in the gonads, has been also found in many somatic tissues, such as liver, spleen, muscles and brain [4,8,9].…”

Section: Introductionmentioning

confidence: 99%

Sex differences in DNA methylation and expression in zebrafish brain: a test of an extended ‘male sex drive’ hypothesis

Chatterjee

Lagisz

Rodger

et al. 2016

Gene

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Sex differences in DNA methylation and expression in zebrafish brain: a test of an extended 'male sex drive ' hypothesis, Gene (2016' hypothesis, Gene ( ), doi: 10.1016' hypothesis, Gene ( /j.gene.2016 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT 3 ABSTRACTThe sex drive hypothesis predicts that stronger selection on male traits has resulted in masculinization of the genome. Here we test whether such masculinizing effects can be detected at the level of the transcriptome and methylome in the adult zebrafish brain.Although methylation is globally similar, we identified 914 specific differentially methylated CpGs (DMCs) between males and females (435 were hypermethylated and 479 were hypomethylated in males compared to females). These DMCs were prevalent in gene body, intergenic regions and CpG island shores. We also discovered 15 distinct CpG clusters with striking sex-specific DNA methylation differences. In contrast, at transcriptome level, more female-biased genes than male-biased genes were expressed, giving little support for the male sex drive hypothesis.Our study provides genome-wide methylome and transcriptome assessment and sheds light on sex-specific epigenetic patterns and in zebrafish for the first time.

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“…Initial microarray experiments comparing gene expression between the sexes in Drosophila revealed that a large portion of the genome is differentially expressed between the sexes, and that there is a significant underrepresentation of male-biased genes (i.e. genes with higher levels of expression in males) on the X chromosome [14][15][16]23]. A similar relationship between sex-biased genes and chromosomal location has been found in other Drosophila species [16,23], including the neo-X chromosome in Drosophila pseudoobscura [16], as well as in mosquitoes [24] and flour beetles [25].…”

Section: Genetic Architecture Of Sexual Dimorphism and Sexual Conflictmentioning

confidence: 99%

“…genes with higher levels of expression in males) on the X chromosome [14][15][16]23]. A similar relationship between sex-biased genes and chromosomal location has been found in other Drosophila species [16,23], including the neo-X chromosome in Drosophila pseudoobscura [16], as well as in mosquitoes [24] and flour beetles [25]. This 'demasculinization' of the X involves extensive gene movement off of the X chromosome on to an autosome, and, therefore, is consistent with the resolution of sexual conflict resulting from genes with dominant effects.…”

Section: Genetic Architecture Of Sexual Dimorphism and Sexual Conflictmentioning

confidence: 99%

Gene duplication, tissue-specific gene expression and sexual conflict in stalk-eyed flies (Diopsidae)

Baker

Narechania

Johns

et al. 2012

Phil. Trans. R. Soc. B

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Gene duplication provides an essential source of novel genetic material to facilitate rapid morphological evolution. Traits involved in reproduction and sexual dimorphism represent some of the fastest evolving traits in nature, and gene duplication is intricately involved in the origin and evolution of these traits. Here, we review genomic research on stalk-eyed flies (Diopsidae) that has been used to examine the extent of gene duplication and its role in the genetic architecture of sexual dimorphism. Stalk-eyed flies are remarkable because of the elongation of the head into long stalks, with the eyes and antenna laterally displaced at the ends of these stalks. Many species are strongly sexually dimorphic for eyespan, and these flies have become a model system for studying sexual selection. Using both expressed sequence tag and next-generation sequencing, we have established an extensive database of gene expression in the developing eye-antennal imaginal disc, the adult head and testes. Duplicated genes exhibit narrower expression patterns than nonduplicated genes, and the testes, in particular, provide an abundant source of gene duplication. Within somatic tissue, duplicated genes are more likely to be differentially expressed between the sexes, suggesting gene duplication may provide a mechanism for resolving sexual conflict.

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Constraint and turnover in sex-biased gene expression in the genus Drosophila

Cited by 280 publications

References 39 publications

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

Sex differences in DNA methylation and expression in zebrafish brain: a test of an extended ‘male sex drive’ hypothesis

Gene duplication, tissue-specific gene expression and sexual conflict in stalk-eyed flies (Diopsidae)

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