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An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
Published on: November 3, 2010
Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human
Kun Zhang1, Jin Billy Li, Yuan Gao
1Department of Bioengineering, University of California at San Diego, La Jolla, California, USA. kzhang@bioeng.ucsd.edu
Nature Methods
|July 22, 2009
Summary
We developed a digital RNA allelotyping method to measure allele-specific gene expression. Genetic variations, not tissue type, primarily drive differences in gene expression ratios.
Area of Science:
- Genomics
- Molecular Biology
- Transcriptomics
Background:
- Allele-specific gene expression (ASE) provides insights into gene regulation.
- Quantitative methods are needed to interrogate ASE across multiple samples.
- Understanding the factors influencing ASE is crucial for deciphering gene regulation.
Purpose of the Study:
- To develop and validate a digital RNA allelotyping method for quantitative ASE analysis.
- To investigate the prevalence and tissue specificity of ASE in human cell lines.
- To determine the relative contributions of genetic variation, tissue type, and growth conditions to ASE.
Main Methods:
- Digital RNA allelotyping using ultra-deep sequencing of padlock-captured single-nucleotide polymorphisms (SNPs).
- Analysis of four cell lines from the Personal Genome Project.
- Comparison of allele-specific expression patterns in sibling versus unrelated human embryonic stem cell lines.
Main Results:
- 11-22% of heterozygous SNPs exhibited allele-specific expression in cell lines.
- 4.3-8.5% of SNPs showed tissue-specific allele-specific expression, indicating cis-regulation.
- Genetic variation explained most of the variation in allelic ratios, surpassing tissue type or growth conditions.
- Allelic ratios are predominantly influenced by cis-regulatory mechanisms on sense transcripts.
Conclusions:
- Digital RNA allelotyping is a robust method for quantitative ASE analysis.
- Genetic variation is a major determinant of allele-specific gene expression.
- Cis-regulatory mechanisms on sense transcripts play a primary role in establishing allelic ratios.
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