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The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance
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 beginn...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4081098/ https://www.ncbi.nlm.nih.gov/pubmed/24895435 http://dx.doi.org/10.1093/nar/gku498 |
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author | Conte, Ivan Merella, Stefania Garcia-Manteiga, Jose Manuel Migliore, Chiara Lazarevic, Dejan Carrella, Sabrina Marco-Ferreres, Raquel Avellino, Raffaella Davidson, Nathan Paul Emmett, Warren Sanges, Remo Bockett, Nicholas Van Heel, David Meroni, Germana Bovolenta, Paola Stupka, Elia Banfi, Sandro |
author_facet | Conte, Ivan Merella, Stefania Garcia-Manteiga, Jose Manuel Migliore, Chiara Lazarevic, Dejan Carrella, Sabrina Marco-Ferreres, Raquel Avellino, Raffaella Davidson, Nathan Paul Emmett, Warren Sanges, Remo Bockett, Nicholas Van Heel, David Meroni, Germana Bovolenta, Paola Stupka, Elia Banfi, Sandro |
author_sort | Conte, Ivan |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-4081098 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-40810982014-07-10 The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance Conte, Ivan Merella, Stefania Garcia-Manteiga, Jose Manuel Migliore, Chiara Lazarevic, Dejan Carrella, Sabrina Marco-Ferreres, Raquel Avellino, Raffaella Davidson, Nathan Paul Emmett, Warren Sanges, Remo Bockett, Nicholas Van Heel, David Meroni, Germana Bovolenta, Paola Stupka, Elia Banfi, Sandro Nucleic Acids Res Genomics 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. Oxford University Press 2014-08-01 2014-06-04 /pmc/articles/PMC4081098/ /pubmed/24895435 http://dx.doi.org/10.1093/nar/gku498 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Genomics Conte, Ivan Merella, Stefania Garcia-Manteiga, Jose Manuel Migliore, Chiara Lazarevic, Dejan Carrella, Sabrina Marco-Ferreres, Raquel Avellino, Raffaella Davidson, Nathan Paul Emmett, Warren Sanges, Remo Bockett, Nicholas Van Heel, David Meroni, Germana Bovolenta, Paola Stupka, Elia Banfi, Sandro The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance |
title | The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance |
title_full | The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance |
title_fullStr | The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance |
title_full_unstemmed | The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance |
title_short | The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance |
title_sort | combination of transcriptomics and informatics identifies pathways targeted by mir-204 during neurogenesis and axon guidance |
topic | Genomics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4081098/ https://www.ncbi.nlm.nih.gov/pubmed/24895435 http://dx.doi.org/10.1093/nar/gku498 |
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