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A genomic bias for genotype-environment interactions in C. elegans
Vladislav Grishkevich1, Shay Ben-Elazar, Tamar Hashimshony
1Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
Molecular Systems Biology
|June 7, 2012
Summary
Organism traits depend on genes and environment. Highly regulated genes, influenced by upstream regulators, show more genotype-environment interactions, explaining gene expression diversity.
Area of Science:
- Genomics
- Developmental Biology
- Evolutionary Biology
Background:
- Organism phenotype results from genotype and environmental interactions.
- Understanding genomic factors driving genotype-environment interactions in gene expression is crucial but limited.
- Gene expression diversity within species is significant but its origins are not fully elucidated.
Purpose of the Study:
- To investigate the genomic properties of genes exhibiting genotype-environment interactions.
- To identify characteristics of genes that are highly regulated and prone to genotype-environment interactions.
- To explore the role of upstream regulators in mediating genotype-environment interactions.
Main Methods:
- Analysis of transcriptomes from five C. elegans strains across five distinct growth conditions.
- Examination of genomic features including intergenic lengths, motif concentration, and expression levels.
- Sequencing of C. elegans strains to identify promoter single-nucleotide polymorphisms (SNPs).
Main Results:
- Highly regulated genes, characterized by intergenic lengths, motif concentration, and expression levels, are predisposed to genotype-environment interactions.
- Genes with expression variation across genotypes are enriched for promoter SNPs.
- Genes with genotype-environment interactions did not show significant enrichment for promoter SNPs compared to the background.
Conclusions:
- The inherent highly regulated nature of specific genes predisposes them to genotype-environment interactions.
- Changes in upstream regulators are likely responsible for mediating genotype-environment interactions in gene expression.
- This finding offers insights into the origins of extensive gene expression diversity in closely related species.
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