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Published on: August 12, 2019
A systematic eQTL study of cis-trans epistasis in 210 HapMap individuals
Jessica Becker1, Jens R Wendland, Britta Haenisch
1Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.
European Journal of Human Genetics : EJHG
|August 18, 2011
Summary
This study reveals that about 15% of transcript expression is significantly regulated by single nucleotide polymorphism (SNP)-SNP interactions, a higher rate than expected. These findings offer new insights into complex genome-transcriptome regulation.
Area of Science:
- Genomics
- Transcriptomics
- Systems Biology
Background:
- Understanding gene regulation is crucial for deciphering complex traits and diseases.
- Single nucleotide polymorphisms (SNPs) are known to influence gene expression, but the role of SNP-SNP interactions (epistasis) is less understood.
Purpose of the Study:
- To identify transcripts regulated by SNP-SNP interactions.
- To investigate the mechanisms underlying cis-trans-regulated gene expression.
- To explore the prevalence and characteristics of epistatic interactions in gene regulation.
Main Methods:
- Analyzed 3107 transcripts and 86,613 linkage disequilibrium-pruned SNP markers in 210 individuals.
- Tested for epistasis between cis-SNPs and trans-SNPs for each transcript.
- Corrected for multiple testing to identify significant cis-trans-regulated expression effects.
Main Results:
- Approximately 15% of transcripts showed expression regulated by significant two-locus SNP interactions, exceeding chance expectations (P = 2.86 × 10(-144)).
- Cis-SNPs with marginal effects were more likely involved in two-locus regulation than expected (P = 8.27 × 10(-05)).
- Gene-mediated trans-effects and enrichment of specific chromosomal regions or cellular processes in epistatic interactions were not supported by the data.
Conclusions:
- SNP-SNP interactions play a significant role in regulating transcript expression.
- The findings challenge the notion of gene-mediated trans-effects as a major source of epistasis in this context.
- Identified cis-trans regulated genes may warrant further investigation for their roles in associated disorders.
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