Digital RNA Allelotyping Reveals Tissue-specific and Allele-specific Gene Expression in Human

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2009 Jul 22

PMID 19620972

Citations 97

Authors

Kun Zhang

Jin Billy Li

Yuan Gao

Dieter Egli

Bin Xie

Jie Deng

Zhe Li

Je-Hyuk Lee

John Aach

Emily M LeProust

Kevin Eggan

George M Church

Affiliations

Soon will be listed here.

Abstract

We developed a digital RNA allelotyping method for quantitatively interrogating allele-specific gene expression. This method involves ultra-deep sequencing of padlock-captured single-nucleotide polymorphisms (SNPs) from the transcriptome. We characterized four cell lines established from two human subjects in the Personal Genome Project. Approximately 11-22% of the heterozygous mRNA-associated SNPs showed allele-specific expression in each cell line and 4.3-8.5% were tissue-specific, suggesting the presence of tissue-specific cis regulation. When we applied allelotyping to two pairs of sibling human embryonic stem cell lines, the sibling lines were more similar in allele-specific expression than were the genetically unrelated lines. We found that the variation of allelic ratios in gene expression among different cell lines was primarily explained by genetic variations, much more so than by specific tissue types or growth conditions. Comparison of expressed SNPs on the sense and antisense transcripts suggested that allelic ratios are primarily determined by cis-regulatory mechanisms on the sense transcripts.

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