title: Gene and noncoding RNA regulation underlying photoreceptor protection: microarray study of dietary antioxidant saffron and photobiomodulation in rat retina.
abstract: OBJECTIVE
  To identify the genes and noncoding RNAs (ncRNAs) involved in the neuroprotective actions of a dietary antioxidant (saffron) and of photobiomodulation (PBM).
  
  
  METHODS
  We used a previously published assay of photoreceptor damage, in which albino Sprague Dawley rats raised in dim cyclic illumination (12 h 5 lux, 12 h darkness) were challenged by 24 h exposure to bright (1,000 lux) light. Experimental groups were protected against light damage by pretreatment with dietary saffron (1 mg/kg/day for 21 days) or PBM (9 J/cm(2) at the eye, daily for 5 days). RNA from one eye of four animals in each of the six experimental groups (control, light damage [LD], saffron, PBM, saffronLD, and PBMLD) was hybridized to Affymetrix rat genome ST arrays. Quantitative real-time PCR analysis of 14 selected genes was used to validate the microarray results.
  
  
  RESULTS
  LD caused the regulation of 175 entities (genes and ncRNAs) beyond criterion levels (p<0.05 in comparison with controls, fold-change >2). PBM pretreatment reduced the expression of 126 of these 175 LD-regulated entities below criterion; saffron pretreatment reduced the expression of 53 entities (50 in common with PBM). In addition, PBM pretreatment regulated the expression of 67 entities not regulated by LD, while saffron pretreatment regulated 122 entities not regulated by LD (48 in common with PBM). PBM and saffron, given without LD, regulated genes and ncRNAs beyond criterion levels, but in lesser numbers than during their protective action. A high proportion of the entities regulated by LD (>90%) were known genes. By contrast, ncRNAs were prominent among the entities regulated by PBM and saffron in their neuroprotective roles (73% and 62%, respectively).
  
  
  CONCLUSIONS
  Given alone, saffron and (more prominently) PBM both regulated significant numbers of genes and ncRNAs. Given before retinal exposure to damaging light, thus while exerting their neuroprotective action, they regulated much larger numbers of entities, among which ncRNAs were prominent. Further, the downregulation of known genes and of ncRNAs was prominent in the protective actions of both neuroprotectants. These comparisons provide an overview of gene expression induced by two neuroprotectants and provide a basis for the more focused study of their mechanisms.
authors.affiliation: Division of Biomedical Sciences & Biochemistry, Research School of Biology, Australian National University, Sydney, Australia. riccardo.natoli@anu.edu.au
authors.forename: Riccardo
authors.initials: R
authors.lastname: Natoli
authors.forename: Yuan
authors.initials: Y
authors.lastname: Zhu
authors.forename: Krisztina
authors.initials: K
authors.lastname: Valter
authors.forename: Silvia
authors.initials: S
authors.lastname: Bisti
authors.forename: Janis
authors.initials: J
authors.lastname: Eells
authors.forename: Jonathan
authors.initials: J
authors.lastname: Stone
mesh_terms: D000818:Animals; D000975:Antioxidants / Q000494:pharmacology*; D016923:Cell Death / Q000187:drug effects; D016000:Cluster Analysis; D027622:Crocus / Q000737:chemistry; D019610:Cytoprotection / Q000187:drug effects / Q000528:radiation effects; D004032:Diet; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000187:drug effects* / Q000528:radiation effects; D007155:Immunologic Factors / Q000494:pharmacology; D008027:Light; D020411:Oligonucleotide Array Sequence Analysis; D020419:Photoreceptor Cells, Vertebrate / Q000166:cytology* / Q000187:drug effects / Q000378:metabolism / Q000528:radiation effects; D022661:RNA, Untranslated / Q000235:genetics*; D051381:Rats; D017207:Rats, Sprague-Dawley; D015203:Reproducibility of Results; D012160:Retina / Q000187:drug effects / Q000378:metabolism* / Q000528:radiation effects; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D000975:Antioxidants; D007155:Immunologic Factors; D022661:RNA, Untranslated