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DeBoever C, Li H, Jakubosky D, Benaglio P, Reyna J, Olson KM, Huang H, Biggs W, Sandoval E, D'Antonio M, Jepsen K, Matsui H, Arias A, Ren B, Nariai N, Smith EN, D'Antonio-Chronowska A, Farley EK, Frazer KA. Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. Cell Stem Cell 2017; 20:533-546.e7. [PMID: 28388430 PMCID: PMC5444918 DOI: 10.1016/j.stem.2017.03.009] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 12/27/2016] [Accepted: 03/15/2017] [Indexed: 12/18/2022]
Abstract
In this study, we used whole-genome sequencing and gene expression profiling of 215 human induced pluripotent stem cell (iPSC) lines from different donors to identify genetic variants associated with RNA expression for 5,746 genes. We were able to predict causal variants for these expression quantitative trait loci (eQTLs) that disrupt transcription factor binding and validated a subset of them experimentally. We also identified copy-number variant (CNV) eQTLs, including some that appear to affect gene expression by altering the copy number of intergenic regulatory regions. In addition, we were able to identify effects on gene expression of rare genic CNVs and regulatory single-nucleotide variants and found that reactivation of gene expression on the X chromosome depends on gene chromosomal position. Our work highlights the value of iPSCs for genetic association analyses and provides a unique resource for investigating the genetic regulation of gene expression in pluripotent cells.
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Affiliation(s)
- Christopher DeBoever
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - He Li
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - David Jakubosky
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093-0419, USA; Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Paola Benaglio
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Joaquin Reyna
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Katrina M Olson
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA; Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Hui Huang
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093-0419, USA; Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | | | | | - Matteo D'Antonio
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Angelo Arias
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Bing Ren
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA; Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Naoki Nariai
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | - Erin N Smith
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093-0419, USA
| | | | - Emma K Farley
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA; Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093-0419, USA.
| | - Kelly A Frazer
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0419, USA; Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093-0419, USA.
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