title: Microarray analysis of XOPS-mCFP zebrafish retina identifies genes associated with rod photoreceptor degeneration and regeneration.
abstract: OBJECTIVE
  XOPS-mCFP transgenic zebrafish experience a continual cycle of rod photoreceptor development and degeneration throughout life, making them a useful model for investigating the molecular determinants of rod photoreceptor regeneration. The purpose of this study was to compare the gene expression profiles of wild-type and XOPS-mCFP retinas and identify genes that may contribute to the regeneration of the rods.
  
  
  METHODS
  Adult wild-type and XOPS-mCFP retinal mRNA was subjected to microarray analysis. Pathway analysis was used to identify biologically relevant processes that were significantly represented in the dataset. Expression changes were verified by RT-PCR. Selected genes were further examined during retinal development and in adult retinas by in situ hybridization and immunohistochemistry and in a transgenic fluorescent reporter line.
  
  
  RESULTS
  More than 600 genes displayed significant expression changes in XOPS-mCFP retinas compared with expression in wild-type controls. Many of the downregulated genes were associated with phototransduction, whereas upregulated genes were associated with several biological functions, including cell cycle, DNA replication and repair, and cell development and death. RT-PCR analysis of a subset of these genes confirmed the microarray
  
  
  RESULTS
  Three transcription factors (sox11b, insm1a, and c-myb), displaying increased expression in XOPS-mCFP retinas, were also expressed throughout retinal development and in the persistently neurogenic ciliary marginal zone.
  
  
  CONCLUSIONS
  This study identified numerous gene expression changes in response to rod degeneration in zebrafish and further suggests a role for the transcriptional regulators sox11b, insm1a, and c-myb in both retinal development and rod photoreceptor regeneration.
authors.affiliation: Department of Biology, University of Kentucky, Lexington, KY 40506, USA. ann.morris@uky.edu
authors.forename: Ann C
authors.initials: AC
authors.lastname: Morris
authors.forename: Marie A
authors.initials: MA
authors.lastname: Forbes-Osborne
authors.forename: Lakshmi S
authors.initials: LS
authors.lastname: Pillai
authors.forename: James M
authors.initials: JM
authors.lastname: Fadool
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified; D005260:Female; D019084:Fluorescent Antibody Technique, Indirect; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000502:physiology*; D049452:Green Fluorescent Proteins / Q000235:genetics*; D017403:In Situ Hybridization; D008297:Male; D046228:Microarray Analysis; D018809:Proliferating Cell Nuclear Antigen / Q000378:metabolism; D020598:Proto-Oncogene Proteins c-myb / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics; D011993:Recombinant Fusion Proteins / Q000235:genetics*; D012038:Regeneration / Q000235:genetics*; D012162:Retinal Degeneration / Q000235:genetics* / Q000378:metabolism / Q000503:physiopathology; D017948:Retinal Rod Photoreceptor Cells / Q000502:physiology*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012243:Rhodopsin / Q000235:genetics*; D055747:SOX Transcription Factors / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism; D019076:Transgenes; D015027:Zebrafish / Q000235:genetics; D029961:Zebrafish Proteins / Q000378:metabolism
chemical_list: C485182:Cyan Fluorescent Protein; C513925:Insm1a protein, zebrafish; D018809:Proliferating Cell Nuclear Antigen; D020598:Proto-Oncogene Proteins c-myb; D012333:RNA, Messenger; D011993:Recombinant Fusion Proteins; D055747:SOX Transcription Factors; D014157:Transcription Factors; D029961:Zebrafish Proteins; C490795:sox11b protein, zebrafish; D049452:Green Fluorescent Proteins; D012243:Rhodopsin