A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells

• Published in: PLoS genetics Vol. 5; no. 11; p. e1000718
• Main Authors: Lee, Je-Hyuk, Park, In-Hyun, Gao, Yuan, Li, Jin Billy, Li, Zhe, Daley, George Q., Zhang, Kun, Church, George M.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.11.2009; Public Library of Science (PLoS)
• Subjects: Alleles; Cell Differentiation; Cell Line; Cells, Cultured; Cluster Analysis; Computational Biology - methods; DNA methylation; DNA, Complementary; Experiments; Flow Cytometry; Gene expression; Gene Expression Regulation - genetics; Gene loci; Genetic aspects; Genetics; Genetics and Genomics/Functional Genomics; Genetics and Genomics/Gene Expression; Genomes; Genotype & phenotype; Human Genome Project; Humans; Induced Pluripotent Stem Cells; Noise; Nucleic Acid Amplification Techniques; Organ Specificity; Proteins; Quantitative trait loci; Regulatory Elements, Transcriptional; Reproducibility of Results; RNA; Skin; Stem cells
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1000718

Normal variation in gene expression due to regulatory polymorphisms is often masked by biological and experimental noise. In addition, some regulatory polymorphisms may become apparent only in specific tissues. We derived human induced pluripotent stem (iPS) cells from adult skin primary fibroblasts and attempted to detect tissue-specific cis-regulatory variants using in vitro cell differentiation. We used padlock probes and high-throughput sequencing for digital RNA allelotyping and measured allele-specific gene expression in primary fibroblasts, lymphoblastoid cells, iPS cells, and their differentiated derivatives. We show that allele-specific expression is both cell type and genotype-dependent, but the majority of detectable allele-specific expression loci remains consistent despite large changes in the cell type or the experimental condition following iPS reprogramming, except on the X-chromosome. We show that our approach to mapping cis-regulatory variants reduces in vitro experimental noise and reveals additional tissue-specific variants using skin-derived human iPS cells.