ZFIN ID: ZDB-PUB-080902-21
Factorial microarray analysis of zebrafish retinal development
Leung, Y.F., Ma, P., Link, B.A., and Dowling, J.E.
Date: 2008
Source: Proceedings of the National Academy of Sciences of the United States of America   105(35): 12909-12914 (Journal)
Registered Authors: Dowling, John E., Leung, Yuk Fai, Link, Brian
Keywords: Brg1-regulated genes, neuronal differentiation, cellular differentiation, signal transduction pathways, transcription factors
Microarrays: GEO:GSE8874
MeSH Terms:
  • Adaptor Proteins, Signal Transducing
  • Animals
  • Cell Cycle
  • Cyclin-Dependent Kinase 5/metabolism
  • DNA Helicases/genetics
  • DNA Helicases/metabolism
  • Gene Expression Regulation, Developmental*
  • Genes, Developmental
  • Microarray Analysis*
  • Models, Genetic
  • Organogenesis
  • Reproducibility of Results
  • Retina/cytology
  • Retina/embryology*
  • Retina/enzymology
  • Signal Transduction
  • Transcription, Genetic
  • Zebrafish/embryology*
  • Zebrafish/genetics*
  • Zebrafish Proteins/genetics
  • Zebrafish Proteins/metabolism
PubMed: 18753621 Full text @ Proc. Natl. Acad. Sci. USA
In a zebrafish recessive mutant young (yng), retinal cells are specified to distinct cell classes, but they fail to morphologically differentiate. A null mutation in a brahma-related gene 1 (brg1) is responsible for this phenotype. To identify retina-specific Brg1-regulated genes that control cellular differentiation, we conducted a factorial microarray analysis. Gene expression profiles were compared from wild-type and yng retinas and stage-matched whole embryos at 36 and 52 hours postfertilization (hpf). From our analysis, three categories of genes were identified: (i) Brg1-regulated retinal differentiation genes (731 probesets), (ii) retina-specific genes independent of Brg1 regulation (3,038 probesets), and (iii) Brg1-regulated genes outside the retina (107 probesets). Biological significance was confirmed by further analysis of components of the Cdk5 signaling pathway and Irx transcription factor family, representing genes identified in category 1. This study highlights the utility of factorial microarray analysis to efficiently identify relevant regulatory pathways influenced by both specific gene products and normal developmental events.