Retinal Cell Type DNA Methylation and Histone Modifications Predict Reprogramming Efficiency and Retinogenesis in 3D Organoid Cultures

Cell Rep. 2018 Mar 6;22(10):2601-2614. doi: 10.1016/j.celrep.2018.01.075.


Diverse cell types can be reprogrammed into pluripotent stem cells by ectopic expression of Oct4 (Pou5f1), Klf4, Sox3, and Myc. Many of these induced pluripotent stem cells (iPSCs) retain memory, in terms of DNA methylation and histone modifications (epigenetic memory), of their cellular origins, and this may bias subsequent differentiation. Neurons are difficult to reprogram, and there has not been a systematic side-by-side characterization of reprogramming efficiency or epigenetic memory across different neuronal subtypes. Here, we compare reprogramming efficiency of five different retinal cell types at two different stages of development. Retinal differentiation from each iPSC line was measured using a quantitative standardized scoring system called STEM-RET and compared to the epigenetic memory. Neurons with the lowest reprogramming efficiency produced iPSC lines with the best retinal differentiation and were more likely to retain epigenetic memory of their cellular origins. In addition, we identified biomarkers of iPSCs that are predictive of retinal differentiation.

Keywords: Meis1; chromHMM; epigenetic memory; epigenetics; iPSCs; reprogramming; retina; retinal organoid.

Publication types

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

MeSH terms

  • Animals
  • Biomarkers / metabolism
  • Cell Culture Techniques
  • Cell Differentiation
  • Cell Nucleus / metabolism
  • Cellular Reprogramming*
  • DNA Methylation*
  • Enhancer Elements, Genetic / genetics
  • Epigenesis, Genetic
  • Histones / metabolism*
  • Induced Pluripotent Stem Cells / metabolism
  • Kruppel-Like Factor 4
  • Mice
  • Organogenesis*
  • Organoids / growth & development*
  • Promoter Regions, Genetic / genetics
  • Protein Processing, Post-Translational*
  • Retina / cytology*
  • Retina / metabolism*


  • Biomarkers
  • Histones
  • Klf4 protein, mouse
  • Kruppel-Like Factor 4