Transcriptional profiling of murine retinas undergoing semi-synchronous cone photoreceptor differentiation

Dev Biol. 2019 Sep 15;453(2):155-167. doi: 10.1016/j.ydbio.2019.05.016. Epub 2019 Jun 1.


Uncovering the gene regulatory networks that control cone photoreceptor formation has been hindered because cones only make up a few percent of the retina and form asynchronously during development. To overcome these limitations, we used a γ-secretase inhibitor, DAPT, to disrupt Notch signaling and force proliferating retinal progenitor cells to rapidly adopt neuronal identity. We treated mouse retinal explants at the peak of cone genesis with DAPT and examined tissues at several time-points by histology and bulk RNA-sequencing. We found that this treatment caused supernumerary cone formation in an overwhelmingly synchronized fashion. This analysis revealed several categorical patterns of gene expression changes over time relative to DMSO treated control explants. These were placed in the temporal context of the activation of Otx2, a transcription factor that is expressed at the onset of photoreceptor development and that is required for both rod and cone formation. One group of interest had genes, such as Mybl1, Ascl1, Neurog2, and Olig2, that became upregulated by DAPT treatment before Otx2. Two other groups showed upregulated gene expression shortly after Otx2, either transiently or permanently. This included genes such as Mybl1, Meis2, and Podxl. Our data provide a developmental timeline of the gene expression events that underlie the initial steps of cone genesis and maturation. Applying this strategy to human retinal organoid cultures was also sufficient to induce a massive increase in cone genesis. Taken together, our results provide a temporal framework that can be used to elucidate the gene regulatory logic controlling cone photoreceptor development.

Keywords: Cone photoreceptor; Fate specification; RNA-Seq; Retinal development; Retinal organoid; γ-secretase inhibition.

Publication types

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

MeSH terms

  • Amyloid Precursor Protein Secretases / antagonists & inhibitors
  • Amyloid Precursor Protein Secretases / metabolism
  • Animals
  • Cell Differentiation / drug effects
  • Cell Differentiation / genetics*
  • Embryo, Mammalian / drug effects
  • Embryo, Mammalian / metabolism
  • Enzyme Inhibitors / pharmacology
  • Female
  • Gene Expression Profiling*
  • Gene Expression Regulation, Developmental / drug effects
  • Humans
  • Mice
  • Organoids / drug effects
  • Organoids / metabolism
  • Otx Transcription Factors / genetics
  • Otx Transcription Factors / metabolism
  • Retinal Cone Photoreceptor Cells / cytology*
  • Retinal Cone Photoreceptor Cells / drug effects
  • Retinal Cone Photoreceptor Cells / metabolism*
  • Time Factors
  • Up-Regulation / drug effects
  • Up-Regulation / genetics


  • Enzyme Inhibitors
  • Otx Transcription Factors
  • Otx2 protein, mouse
  • Amyloid Precursor Protein Secretases