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

Elife. 2015 Jun 23;4:e07103. doi: 10.7554/eLife.07103.

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 within-species 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.

Keywords: Pan troglodytes; cell panel; chimpanzee; developmental biology; evolutionary biology; genomics; human; iPSC; induced pluripotent stem cells; stem cells.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Differentiation*
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental
  • Genomics / methods*
  • Humans
  • Induced Pluripotent Stem Cells*
  • Molecular Sequence Data
  • Pan troglodytes*
  • Sequence Analysis, DNA

Associated data

  • GEO/GSE61343