Gene expression profiling of zebrafish embryonic retinal pigment epithelium in vivo

Invest Ophthalmol Vis Sci. 2007 Feb;48(2):881-90. doi: 10.1167/iovs.06-0723.


Purpose: Eye development and photoreceptor maintenance is dependent on the retinal pigment epithelium (RPE), a thin layer of cells that underlies the neural retina. Despite its importance, development of RPE has not been studied by a genomic approach. In this study, a microarray expression-profiling methodology was established for studying RPE development.

Methods: The intact retina with RPE attached was dissected from developing embryos, and differentially expressed genes in RPE were inferred by comparing the dissected tissues with retinas without RPE, in microarray and statistical analyses.

Results: Of the probesets used, 8810 were significantly expressed in RPE at 52 hours postfertilization (hpf), of which 1443 may have biologically meaningful expression levels. Further, 78 and 988 probesets were found to be significantly over- or underexpressed in RPE, respectively, compared with retina. Also, 79.2% (38/48) of the known overexpressed probesets were independently validated as RPE-related transcripts.

Conclusions: The results strongly suggest that this methodology can obtain in vivo RPE-specific gene expression from the zebrafish embryos and identify novel RPE markers.

Publication types

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

MeSH terms

  • Animals
  • Embryo, Nonmammalian / metabolism*
  • Eye Proteins / genetics
  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Developmental / physiology*
  • Oligonucleotide Array Sequence Analysis / methods
  • Pigment Epithelium of Eye / embryology*
  • RNA / isolation & purification
  • Retina / embryology
  • Zebrafish / embryology*
  • Zebrafish Proteins / genetics*


  • Eye Proteins
  • Zebrafish Proteins
  • RNA