title: microRNA regulatory circuits in a mouse model of inherited retinal degeneration.
abstract: miRNA dysregulation is a hallmark of many neurodegenerative disorders, including those involving the retina. Up-regulation of miR-1/133 and miR-142, and down-regulation of miR-183/96/182 has been described in the RHO-P347S mouse retina, a model for a common form of inherited blindness. High-throughput LC-MS/MS was employed to analyse the protein expression of predicted targets for these miRNAs in RHO-P347S mouse retinas; 133 potential target genes were identified. Pathway over-representation analysis suggests G-protein signaling/visual transduction, and synaptic transmission for miR-1, and transmembrane transport, cell-adhesion, signal transduction and apoptosis for miR-183/96/182 as regulated functions in retina. Validation of miRNA-target mRNA interactions for miR-1, miR-96/182 and miR-96 targeting Ctbp2, Rac1 and Slc6a9, respectively, was demonstrated in vitro. In vivo interaction of miR-183/96/182 and Rac1 mRNA in retina was confirmed using miR-CATCH. Additional miRNAs (including miR-103-3p, miR-9-5p) were both predicted to target Rac1 mRNA and enriched by Rac1-miR-CATCH. Other Rac1-miR-CATCH-enriched miRNAs (including miR-125a/b-5p, miR-378a-3p) were not predicted to target Rac1. Furthermore, levels of ~25% of the retinal Rac1 interactors were determined by LC-MS/MS; expression of Rap1gds1 and Cav1 was elevated. Our data suggest significant utilisation of miRNA-based regulation in retina. Possibly more than 30 miRNAs interact with Rac1 in retina, targeting both UTRs and coding regions.
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Arpad
authors.initials: A
authors.lastname: Palfi
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Karsten
authors.initials: K
authors.lastname: Hokamp
authors.affiliation: Research Unit Protein Science, Helmholtz Zentrum Munchen - German Research Center for Environmental Health (GmbH), Neuherberg, Germany.
authors.forename: Stefanie M
authors.initials: SM
authors.lastname: Hauck
authors.affiliation: Respiratory Research Division, Dept. Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Vencken
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Sophia
authors.initials: S
authors.lastname: Millington-Ward
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Naomi
authors.initials: N
authors.lastname: Chadderton
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Mathew
authors.initials: M
authors.lastname: Carrigan
authors.affiliation: Institute of Ophthalmic Research, Center for Ophthalmology, University of Tubingen, Tubingen, Germany.
authors.forename: Elod
authors.initials: E
authors.lastname: Kortvely
authors.affiliation: Respiratory Research Division, Dept. Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin 9, Ireland.
authors.forename: Catherine M
authors.initials: CM
authors.lastname: Greene
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Paul F
authors.initials: PF
authors.lastname: Kenna
authors.affiliation: Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: G Jane
authors.initials: GJ
authors.lastname: Farrar
mesh_terms: D000818:Animals; D002853:Chromatography, Liquid; D004195:Disease Models, Animal; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D051379:Mice; D035683:MicroRNAs / Q000032:analysis*; D012160:Retina / Q000473:pathology*; D012162:Retinal Degeneration / Q000473:pathology*; D053719:Tandem Mass Spectrometry
chemical_list: D035683:MicroRNAs