Factorial microarray analysis of zebrafish retinal development

doi:10.1073/pnas.0806038105

Factorial microarray analysis of zebrafish retinal development

^†Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138;
^‡Department of Biological Sciences, Purdue University, West Lafayette, IN 47907;
^‖Department of Statistics and
^††Institute for Genomic Biology, University of Illinois, Champaign, IL 61820; and
^‡‡Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226

Contributed by John E. Dowling, June 22, 2008
↵^§Y.F.L. and P.M. contributed equally to this work. (received for review April 17, 2008)

Abstract

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.

Footnotes

^¶To whom correspondence may addressed. E-mail: yfleung{at}purdue.edu or dowling{at}mcb.harvard.edu
Author contributions: Y.F.L., P.M., B.A.L., and J.E.D. designed research; Y.F.L. performed research; Y.F.L., P.M., B.A.L., and J.E.D. analyzed data; and Y.F.L., P.M., B.A.L., and J.E.D. wrote the paper.
The authors declare no conflict of interest.
Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE8874).
This article contains supporting information online at www.pnas.org/cgi/content/full/0806038105/DCSupplemental.