A panel of induced pluripotent stem cells from chimpanzees: A resource for comparative functional genomics

Irene Gallego Romero, Bryan J. Pavlovic, Irene Hernando-Herraez, Xiang Zhou, Michelle C. Ward, Nicholas E. Banovich, Courtney L. Kagan, Jonathan E. Burnett, Constance H. Huang, Amy Mitrano, Claudia I. Chavarria, Inbar Friedrich Ben-Nun, Yingchun Li, Karen Sabatini, Trevor R. Leonardo, Mana Parast, Tomas Marques-Bonet, Louise C. Laurent, Jeanne F. Loring, Yoav Gilad

Research output: Contribution to journalArticle

42 Scopus citations

Abstract

Comparative genomics studies in primates are restricted due to our limited access to samples. In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must have access to faithful model systems for a wide range of cell types. To facilitate this, we generated a panel of 7 fully characterized chimpanzee induced pluripotent stem cell (iPSC) lines derived from healthy donors. To demonstrate the utility of comparative iPSC panels, we collected RNA-sequencing and DNA methylation data from the chimpanzee iPSCs and the corresponding fibroblast lines, as well as from 7 human iPSCs and their source lines, which encompass multiple populations and cell types. We observe much less withinspecies variation in iPSCs than in somatic cells, indicating the reprogramming process erases many inter-individual differences. The low within-species regulatory variation in iPSCs allowed us to identify many novel inter-species regulatory differences of small magnitude.

Original languageEnglish (US)
Article numbere07103
Pages (from-to)1-29
Number of pages29
JournaleLife
Volume4
Issue numberJUNE 2015
DOIs
StatePublished - Jun 23 2015
Externally publishedYes

ASJC Scopus subject areas

  • Neuroscience(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)

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    Romero, I. G., Pavlovic, B. J., Hernando-Herraez, I., Zhou, X., Ward, M. C., Banovich, N. E., Kagan, C. L., Burnett, J. E., Huang, C. H., Mitrano, A., Chavarria, C. I., Ben-Nun, I. F., Li, Y., Sabatini, K., Leonardo, T. R., Parast, M., Marques-Bonet, T., Laurent, L. C., Loring, J. F., & Gilad, Y. (2015). A panel of induced pluripotent stem cells from chimpanzees: A resource for comparative functional genomics. eLife, 4(JUNE 2015), 1-29. [e07103]. https://doi.org/10.7554/eLife.07103.001