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A genomic signature of gene-environment interactions in C. elegans

ABSTRACT: The phenotype is an interplay between genetic and environmental components, however the relationship between these two is difficult to predict. For any particular environment only a handful of genes show gene environment interaction [refs]. This may imply that certain constrains prevent genes to participate in gene environment interaction that possibly could be used to predict potential targets for such interaction under different sets of environmental conditions. Our approach was to culture 6 C. elegans strains (5 geographical isolates + 1 mutant straint) at 20Â°C, then split the culture into 5 conditions. We measured mRNA abundances in 4-cell stage embryos using microarray with three separately collected 50-embryo replicates collected for each combination of strain and environment. 90 microarrays of C. elegans for 6 strains * 5 conditions in triplicates.

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Itai Yanai

PROVIDER: E-GEOD-34650 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Heat stress reveals heritable changes in mRNA profile in 4-cell stage embryos of the nematode Caenorhabditis elegans.

Project description:For centuries, scientists have wondered whether the responses of animals and plants to environmental change can be transmitted to subsequent generations. Lately, there been much interest in the inheritance of information that is not encoded by differences in DNA sequence. Here we show that transient, mild heat stress results in a heritable change in the messenger RNA profile of early-stage C. elegans embryos. After heat stress is removed for one generation, abundances of most, but not all, mRNAs have relaxed to the unstressed state. Our approach was to culture worms at 20°C, then split the culture into 20°C control and 25°C treatment, followed by return of the 25°C culture to 20°C. Specifically, we compared mRNA abundances in 4-cell stage embryos collected from mothers kept at 20°C, with embryos whose mothers were also reared at 20°C but whose grandparents had been reared at 25°C. Two strains and two generations under a treatment and under a control condition were analyzed by microarray with three separately collected 50-embryo replicates for each combination, for a total of 24 samples.

2011-12-31 | E-GEOD-30666 | biostudies-arrayexpress

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2010-05-06 | E-GEOD-15233 | biostudies-arrayexpress

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Project description:To identify differences in gene expression patterns between C. elegans and C. briggsae we designed whole-genome species-specific microarrays. We designed two organism-specific microarrays which were then manufactured by Agilent as 44k arrays. Probes were designed to target the coding region, preferentially near the 3’ end, as well as in the presumptive 3’ UTR, up to 150bp downstream of the stop codon. 50-60mer probes were determined using OligoWiz (Wernersson and Nielsen 2005) which selects oligos based upon their cross-hybridization to other coding sequences, Tm, position along the transcript, folding potential, and low-complexity in the sequence. The probes were also restricted against spanning splice junctions to avoid missing transcripts due to errors in gene structure predictions. Each gene was assigned between one and five probes, where the probe with the best overall score was selected as the ‘A-probe’, and the remaining ranked ‘B’ through ‘E’.

2009-08-31 | E-GEOD-15234 | biostudies-arrayexpress

C. briggsae and C. elegans developmental timecourses

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2009-08-31 | E-GEOD-15551 | biostudies-arrayexpress

Global proteomics analysis reveals a role for histone variant H3.3 in the response to starvation

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2011-11-22 | E-GEOD-29896 | biostudies-arrayexpress

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