title: The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance.
abstract: Vertebrate organogenesis is critically sensitive to gene dosage and even subtle variations in the expression levels of key genes may result in a variety of tissue anomalies. MicroRNAs (miRNAs) are fundamental regulators of gene expression and their role in vertebrate tissue patterning is just beginning to be elucidated. To gain further insight into this issue, we analysed the transcriptomic consequences of manipulating the expression of miR-204 in the Medaka fish model system. We used RNA-Seq and an innovative bioinformatics approach, which combines conventional differential expression analysis with the behavior expected by miR-204 targets after its overexpression and knockdown. With this approach combined with a correlative analysis of the putative targets, we identified a wider set of miR-204 target genes belonging to different pathways. Together, these approaches confirmed that miR-204 has a key role in eye development and further highlighted its putative function in neural differentiation processes, including axon guidance as supported by in vivo functional studies. Together, our results demonstrate the advantage of integrating next-generation sequencing and bioinformatics approaches to investigate miRNA biology and provide new important information on the role of miRNAs in the control of axon guidance and more broadly in nervous system development.
authors.affiliation: Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy.
authors.forename: Ivan
authors.initials: I
authors.lastname: Conte
authors.affiliation: Center For Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina, 58, 20132 Milan, Italy.
authors.forename: Stefania
authors.initials: S
authors.lastname: Merella
authors.affiliation: Center For Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina, 58, 20132 Milan, Italy.
authors.forename: Jose Manuel
authors.initials: JM
authors.lastname: Garcia-Manteiga
authors.affiliation: CBM Scrl, c/o Area Science Park, Basovizza, 30143 Trieste, Italy.
authors.forename: Chiara
authors.initials: C
authors.lastname: Migliore
authors.affiliation: Center For Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina, 58, 20132 Milan, Italy.
authors.forename: Dejan
authors.initials: D
authors.lastname: Lazarevic
authors.affiliation: Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Carrella
authors.affiliation: Centro de Biología Molecular 'Severo Ochoa', CSIC-UAM, c/Nicolas Cabrera 1, Madrid 28049, Spain CIBER de Enfermedades Raras (CIBERER), c/ Nicolas Cabrera 1, Madrid 28049, Spain.
authors.forename: Raquel
authors.initials: R
authors.lastname: Marco-Ferreres
authors.affiliation: Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy.
authors.forename: Raffaella
authors.initials: R
authors.lastname: Avellino
authors.affiliation: Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy.
authors.forename: Nathan Paul
authors.initials: NP
authors.lastname: Davidson
authors.affiliation: UCL Cancer Institute, Huntley Street, University College London, London WC1E 6BT, UK.
authors.forename: Warren
authors.initials: W
authors.lastname: Emmett
authors.affiliation: Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
authors.forename: Remo
authors.initials: R
authors.lastname: Sanges
authors.affiliation: Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Bockett
authors.affiliation: Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
authors.forename: David
authors.initials: D
authors.lastname: Van Heel
authors.affiliation: CBM Scrl, c/o Area Science Park, Basovizza, 30143 Trieste, Italy.
authors.forename: Germana
authors.initials: G
authors.lastname: Meroni
authors.affiliation: Centro de Biología Molecular 'Severo Ochoa', CSIC-UAM, c/Nicolas Cabrera 1, Madrid 28049, Spain CIBER de Enfermedades Raras (CIBERER), c/ Nicolas Cabrera 1, Madrid 28049, Spain.
authors.forename: Paola
authors.initials: P
authors.lastname: Bovolenta
authors.affiliation: Center For Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Via Olgettina, 58, 20132 Milan, Italy stupka.elia@hsr.it.
authors.forename: Elia
authors.initials: E
authors.lastname: Stupka
authors.affiliation: Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy Medical Genetics, Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, 80138 Naples, Italy banfi@tigem.it.
authors.forename: Sandro
authors.initials: S
authors.lastname: Banfi
mesh_terms: D000818:Animals; D001369:Axons / Q000502:physiology* / Q000648:ultrastructure; D019295:Computational Biology; D020869:Gene Expression Profiling; D055785:Gene Knockdown Techniques; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000378:metabolism*; D023421:Models, Animal; D055495:Neurogenesis / Q000235:genetics*; D009990:Oryzias / Q000196:embryology / Q000235:genetics* / Q000378:metabolism; D012160:Retina / Q000196:embryology / Q000378:metabolism / Q000648:ultrastructure; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs