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Related Experiment Video

Updated: Apr 28, 2026

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Allele-specific expression and eQTL analysis in mouse adipose tissue.

Yehudit Hasin-Brumshtein1, Farhad Hormozdiari, Lisa Martin

  • 1Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA. yehudit.hasin@gmail.com.

BMC Genomics
|June 15, 2014
PubMed
Summary

This study reveals that allele specific expression (ASE) analysis using RNAseq offers a more accurate method for identifying cis-eQTLs compared to traditional local-eQTL mapping. Findings suggest many local-eQTLs may actually be trans interactions.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Systems Biology

Background:

  • Distinguishing cis-eQTLs (cis-acting expression quantitative trait loci) from trans-eQTLs is crucial for understanding gene regulation mechanisms.
  • Historically, technical limitations led to the use of genomic distance-based definitions (local-eQTLs) as a proxy for cis-eQTLs, potentially conflating distinct regulatory effects.

Purpose of the Study:

  • To compare cis-eQTLs identified through allele specific expression (ASE) with local-eQTLs derived from previous studies.
  • To evaluate the accuracy and sensitivity of ASE analysis for eQTL mapping.
  • To investigate potential reasons for discrepancies between cis-eQTL and local-eQTL mapping approaches.

Main Methods:

  • Utilized RNA sequencing to perform allele specific expression (ASE) analysis in adipose tissue of male and female F1 hybrid mice (C57BL/6J x DBA/2J).

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  • Compared ASE-derived cis-eQTLs with local-eQTLs from prior population-based studies in mouse adipose tissue.
  • Integrated ENCODE data to assess the relationship between ASE genes and regulatory elements like DNase I hypersensitive sites.

    • Main Results:

    • Demonstrated poor overlap between cis-eQTLs identified by ASE and local-eQTLs from previous studies, despite high concordance between the two local-eQTL studies.
    • Found that only 15-20% of local-eQTLs were identified as cis by ASE, and less than 50% of ASE genes were recovered in local-eQTL studies.
    • Observed a significant, ASE direction-specific bias for SNPs within DNase I hypersensitive sites among ASE genes.

    Conclusions:

    • Proposed a novel, more sensitive, and accurate ASE analysis approach compared to traditional statistical methods (Fisher's exact test, chi-square test).
    • Concluded that technical differences, such as genomic background or sex specificity, explain only a small fraction of the observed discrepancies.
    • Suggested that the divergence between cis-eQTL and local-eQTL mapping methods could aid in classifying SNP-eQTL interactions into true cis and trans categories, implying many local-eQTLs may represent trans effects.