Unknown,Transcriptomics,Genomics,Proteomics

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Evolution of gene expression in the Drosophila melanogaster subgroup update and extension

ABSTRACT: http://www.nature.com/ng/journal/v33/n2/abs/ng1086.html. Little is known about broad patterns of variation and evolution of gene expression during any developmental process. Here we investigate variation in genome-wide gene expression among Drosophila simulans, Drosophila yakuba and four strains of Drosophila melanogaster during a major developmental transition?the start of metamorphosis. Differences in gene activity between these lineages follow a phylogenetic pattern, and 27% of all of the genes in these genomes differ in their developmental gene expression between at least two strains or species. We identify, on a gene-by-gene basis, the evolutionary forces that shape this variation and show that, both within the transcriptional network that controls metamorphosis and across the whole genome, the expression changes of transcription factor genes are relatively stable, whereas those of their downstream targets are more likely to have evolved. Our results demonstrate extensive evolution of developmental gene expression among closely related species. Extended from the original publication by updating annotation to release 4.0 and using 8 arrays for each strain/species. All Drosophila yakuba arrays are new. see also: PMID: 15122255. http://www.nature.com/ng/journal/v36/n6/abs/ng1355.html Gu Z, Rifkin SA, White KP, Li WH Duplicate genes increase gene expression diversity within and between species.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Scott Rifkin

PROVIDER: E-GEOD-2642 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression.

Rifkin Scott A SA Houle David D Kim Junhyong J White Kevin P KP

Nature 20051101 7065

Mutation is the ultimate source of biological diversity because it generates the variation that fuels evolution. Gene expression is the first step by which an organism translates genetic information into developmental change. Here we estimate the rate at which mutation produces new variation in gene expression by measuring transcript abundances across the genome during the onset of metamorphosis in 12 initially identical Drosophila melanogaster lines that independently accumulated mutations for ...[more]

PMID: 16281035

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Project description:Aims of study: (1) To identify systemic differences in osteoarthritic (OA) bone that contribute to OA pathogenesis. (2) Identify novel osteoporotic (OP) bone-related disease genes. Study involved comparison of trabecular bone extracted from the intertrochanteric (IT) region of the proximal femur (PF) from OA, OP and normal/control (CTL) individuals. Bone was obtained from OA and OP individuals at surgery for total hip replacement and from CTL individuals at autopsy. Keywords: Bone tissue comparison, diseased versus non-diseased, factorial design, linear modelling Four sets of sample comparisons (39 comparisons in total) were made in this study. These comprised 10 OA-CTL female, 10 OA-CTL male, 10 OA-OP female and 9 OP-CTL female comparisons. A Compugen Human 19K-oligo library spotted onto glass slides by the Adelaide Microarray facility (AMF) was used in this study. The slides were interrogated by competitive hybridisation of Cy3 and Cy5 labelled pairs of OA-CTL, OA-OP or OP-CTL amplified RNA samples. Sample pairs were age-matched as closely as possible. A biological dye-swap strategy was employed. After hybridisation and washing of the slides they were scanned using a GenePix 4000B Scanner driven by GenePix Pro 4.0. All analyses were performed using the statistical programming and graphics environment R. The “SPOT” software package was used to identify spots by adaptive segmentation method and subtract backgrounds utilising morphological opening approach. Data analysis was performed in R using Bioconductor. Loess print tip method was used to correct for dye-bias and intensity within each group of adjacent spots printed by one pin. Linear modelling was performed with the Limma package of Bioconductor. Linear models were used to incorporate all available data into a single analysis. This allowed the use of both direct and indirect comparisons in calculation of expression ratios as well as improved accuracy in estimation of variance for each gene. Factorial design utilised the following factors: medical condition (OA or OP or CTL); sex (male or female) for OA patients only.

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Evolution of gene expression in the Drosophila melanogaster subgroup update and extension

Publications

A mutation accumulation assay reveals a broad capacity for rapid evolution of gene expression.

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