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Genome features of “Dark-fly”, a Drosophila line reared long-term in a dark environment

ABSTRACT: To address the molecular mechanisms underlying environmental adaptation, we studied a Drosophila melanogaster line, termed Dark-fly, which has been maintained in constant dark conditions for 57 years (1400 generations).The structural gene copy number changes between the dark fly and its control were assessed by aCGH array. The comparison showed that hundreds of genes in the dark fly bear duplications or deletions relative to the control line.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE35418 | GEO | 2012/01/31

SECONDARY ACCESSION(S): PRJNA152577

REPOSITORIES: GEO

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Genome features of “Dark-fly”, a Drosophila line reared long-term in a dark environment

Project description:To address the molecular mechanisms underlying environmental adaptation, we studied a Drosophila melanogaster line, termed Dark-fly, which has been maintained in constant dark conditions for 57 years (1400 generations).The structural gene copy number changes between the dark fly and its control were assessed by aCGH array. The comparison showed that hundreds of genes in the dark fly bear duplications or deletions relative to the control line. The copy number increase and decrease in the dark flies were determined by two-channel array hybridization with the control line. In addition to biological replicates, a Cy5-Cy3 dye swap was performed.Self-hybridization was also conducted to serve as a quality control.

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P46DR (dark reared) mouse non-deprived vs. deprived visual cortex

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Transcription profiling of mouseP46DR dark reared mouse non-deprived vs. deprived visual cortex

Project description:Wild-type (C57Bl6) mice were dark reared from birth to P42, then underwent monocular enucleation at P42. They were then placed in a normal light-dark environment for 4 days, after which they were sacrificed (at P46). Visual cortex was dissected from 1-mm thick coronal sections, and total RNA was extracted from the tissue lysate using Trizol (Gibco-BRL). Experiment Overall Design: Gene expression in pooled samples from 2 non-deprived (ipsilateral to monocular enucleation) and 2 deprived (contralateral to monocular enucleation) visual hemispheres was compared. Note: two additional cross-animal comparisons were made.

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Transcriptome profiling of dark grown photoreceptor mutants of Arabidopsis.

Project description:Phytochromes mediate a profound developmental shift when dark-grown seedlings are exposed to light. Here we show that a subset of genes is up regulated in phytochrome B (phyB) mutants even before dark-grown seedlings are exposed to light. Most of these genes bear the RY cis motif, which is a binding site of the transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3), and the phyB mutation also enhanced ABI3 expression. These changes in transcriptome have physiological consequences as seedlings of the abi3 mutant showed enhanced responses to pulses of far-red light, while ABI3 overexpressers exhibited the opposite pattern. Seedlings of the wild type derived from seeds germinated in full darkness showed enhanced expression of genes bearing the RY cis motif and reduced responses to far-red light. We propose that, via changes in ABI3 expression, light, perceived mainly by phyB in the seed, generates a downstream trans-developmental phase signal that pre-conditions the seedling to its most likely environment. Keywords: Arabidopsis, photoreceptors, light signal transduction, environmental responses

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