Biological Sciences Division
Published June 23, 2015 | Version v1
Journal article Open

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

Creators

  • 1. University of Chicago
  • 2. Institut de Biologia Evolutiva
  • 3. University of Michigan
  • 4. The Scripps Research Institute
  • 5. University of California San Diego

Description

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.

Data availability

The following data sets were generated:

Gallego Romero I Pavlovic BJ Hernando-Herraez I Banovich NE Kagan CL Burnett JE Huang CH Mitrano A Chavarria CI Ben-Nun I FLi Y Sabatini K Leonardo TR Parast M Marques-Bonet T Laurent LC Loring JF Gilad Y (2014) Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics (RNA-Seq) Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSE60996). http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60996

Gallego Romero I Pavlovic BJ Hernando-Herraez I Banovich NE Kagan CL Burnett JE Huang CH Mitrano A Chavarria CI Ben-Nun IF Li Y Sabatini K Leonardo TR Parast M Marques-Bonet T Laurent LC Loring JF Gilad Y (2014) Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics (methylation array) Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSE61342). http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61342

Gallego Romero I Pavlovic BJ Hernando-Herraez I Zhou X Ward MC Banovich NE Kagan CL Burnett JE Huang CH Mitrano A Chavarria CI Ben-Nun IF Li Y Sabatini K Leonardo TR Parast M Marques-Bonet T Laurent LC Loring JF Gilad Y (2015) Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSE69919). http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69919

The following previously published data sets were used:

Marchetto MC Narvaiza I Denli AM Benner C Gage FH (2013) Differential LINE-1 retrotransposition in induced pluripotent stem cells between humans and great apes Publicly available at the NCBI Gene Expression Omnibus (Accession no: GSE47626). http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47626

Roadmap Epigenomics Consortium Kundaje Meuleman A Ernst W Bilenky J Yen M Heravi-Moussavi A Kheradpour A Zhang P Wang JZ et al. (2015) NIH Epigenomics Roadmap Initiative Publicly available at the NCBI Gene Expression Omnibus (Accession no: PRJNA34535). http://www.ncbi.nlm.nih.gov/bioproject/PRJNA34535

Files

elife-07103-v2.pdf

Files (12.1 MB)

Name Size Download all
Article
md5:f6b533cde575776a6ee2dc3f1f558809
3.5 MB Preview Download
md5:5221af04338619f468dc3d37eaecffe9
8.6 MB Preview Download

Additional details

Identifiers

DOI
10.7554/eLife.07103.001
Other
oai:uchicago.tind.io:9879

Funding

Wellcome Trust
Sir Henry Wellcome Postdoctoral Fellowship
National Institutes of Health
GM077959
California Institute for Regenerative Medicine
CL1-00502
California Institute for Regenerative Medicine
TR01250
European Research Council
Starting Grant
Ministerio de Economía y Competitividad
BFU2011-28549
University of California, San Diego
Generalitat de Catalunya
National Institutes of Health
Training Grant
National Institutes of Health
Training Grant
National Institutes of Health
K12 HD001259
EMBO
ALTF 751-2014
National Center for Advancing Translational Sciences
Clinical and Translational Science Awards, TL1 pre-doctoral fellowship

UChicago Information

Division(s)
Biological Sciences Division
Department(s)
Human Genetics