Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human - PubMed (original) (raw)

doi: 10.1038/nmeth.1357. Epub 2009 Jul 20.

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

Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human

Kun Zhang et al. Nat Methods. 2009 Aug.

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.

PubMed Disclaimer

Figures

Figure 1

Figure 1

Digital allelotyping with padlock probes. (a) The design of padlock probe (top) and a schematic diagram of padlock capturing experiments (bottom). (b) (c) The experimental and analytic workflow of digital allelotyping assay.

Figure 2

Figure 2

Allele-specific expression in human cell lines of various degrees of genetic and phenotypic similarities. (a) Consistency of allelic ratios between two technical replicates. (b–d) Tissue-specific ASE among three PGP1 cell lines of the same genetic background. (e, f) Hierarchical clustering of samples based on allelic ratios or genetic identity. (g) Correlation between the allelic ratio similarity and genetic similarity.

Figure 3

Figure 3

X-inactivation in female human embryonic stem cell lines (HUES37 and HUES58). HUES37 (a). and HUES58 (b). The x-axes are chromosomal positions for the SNPS and the y-axes are the allelic ratios for the M-alleles. Red triangles represent the SNPs that were called monoallelic; blue circles are the SNPs called as allele-specific; and the gray diamonds are the SNPs with bi-allelic expression.

Similar articles

Cited by

References

    1. Yan H, Yuan W, Velculescu VE, et al. Science. 2002;297(5584):1143. - PubMed
    1. Pastinen T, Hudson TJ. Science. 2004;306(5696):647. - PubMed
    1. Lo HS, Wang Z, Hu Y, et al. Genome Res. 2003;13(8):1855. - PMC - PubMed
    1. Knight JC, Keating BJ, Rockett KA, et al. Nat Genet. 2003;33(4):469. - PubMed
    1. Serre D, Gurd S, Ge B, et al. PLoS Genet. 2008;4(2):e1000006. - PMC - PubMed

Publication types

MeSH terms

Substances

Grants and funding

LinkOut - more resources