1
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Mantica F, Iñiguez LP, Marquez Y, Permanyer J, Torres-Mendez A, Cruz J, Franch-Marro X, Tulenko F, Burguera D, Bertrand S, Doyle T, Nouzova M, Currie PD, Noriega FG, Escriva H, Arnone MI, Albertin CB, Wotton KR, Almudi I, Martin D, Irimia M. Evolution of tissue-specific expression of ancestral genes across vertebrates and insects. Nat Ecol Evol 2024:10.1038/s41559-024-02398-5. [PMID: 38622362 DOI: 10.1038/s41559-024-02398-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/08/2024] [Indexed: 04/17/2024]
Abstract
Regulation of gene expression is arguably the main mechanism underlying the phenotypic diversity of tissues within and between species. Here we assembled an extensive transcriptomic dataset covering 8 tissues across 20 bilaterian species and performed analyses using a symmetric phylogeny that allowed the combined and parallel investigation of gene expression evolution between vertebrates and insects. We specifically focused on widely conserved ancestral genes, identifying strong cores of pan-bilaterian tissue-specific genes and even larger groups that diverged to define vertebrate and insect tissues. Systematic inferences of tissue-specificity gains and losses show that nearly half of all ancestral genes have been recruited into tissue-specific transcriptomes. This occurred during both ancient and, especially, recent bilaterian evolution, with several gains being associated with the emergence of unique phenotypes (for example, novel cell types). Such pervasive evolution of tissue specificity was linked to gene duplication coupled with expression specialization of one of the copies, revealing an unappreciated prolonged effect of whole-genome duplications on recent vertebrate evolution.
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Affiliation(s)
- Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Luis P Iñiguez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Yamile Marquez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jon Permanyer
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Torres-Mendez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Josefa Cruz
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Xavier Franch-Marro
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Frank Tulenko
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Demian Burguera
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins; BIOM, Banyuls-sur-Mer, France
| | - Toby Doyle
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Marcela Nouzova
- Institute of Parasitology, CAS, České Budějovice, Czech Republic
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- EMBL Australia; Victorian Node, Monash University, Clayton, Victoria, Australia
| | - Fernando G Noriega
- Biology and BSI, Florida International University, Miami, FL, USA
- Department of Parasitology, University of South Bohemia, České Budějovice, Czech Republic
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins; BIOM, Banyuls-sur-Mer, France
| | | | - Caroline B Albertin
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Karl R Wotton
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Isabel Almudi
- Department of Genetics, Microbiology and Statistics and IRBio, Universitat de Barcelona, Barcelona, Spain
| | - David Martin
- Institute of Evolutionary Biology (IBE, CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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2
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Burguera D, Dionigi F, Kverková K, Winkler S, Brown T, Pippel M, Zhang Y, Shafer M, Nichols ALA, Myers E, Němec P, Musilova Z. Expanded olfactory system in ray-finned fishes capable of terrestrial exploration. BMC Biol 2023; 21:163. [PMID: 37525196 PMCID: PMC10392011 DOI: 10.1186/s12915-023-01661-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/12/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Smell abilities differ greatly among vertebrate species due to distinct sensory needs, with exceptional variability reported in the number of olfactory genes and the size of the odour-processing regions of the brain. However, key environmental factors shaping genomic and phenotypic changes linked to the olfactory system remain difficult to identify at macroevolutionary scales. Here, we investigate the association between diverse ecological traits and the number of olfactory chemoreceptors in approximately two hundred ray-finned fishes. RESULTS We found independent expansions producing large gene repertoires in several lineages of nocturnal amphibious fishes, generally able to perform active terrestrial exploration. We reinforced this finding with on-purpose genomic and transcriptomic analysis of Channallabes apus, a catfish species from a clade with chemosensory-based aerial orientation. Furthermore, we also detected an augmented information-processing capacity in the olfactory bulb of nocturnal amphibious fishes by estimating the number of cells contained in this brain region in twenty-four actinopterygian species. CONCLUSIONS Overall, we report a convergent genomic and phenotypic magnification of the olfactory system in nocturnal amphibious fishes. This finding suggests the possibility of an analogous evolutionary event in fish-like tetrapod ancestors during the first steps of the water-to-land transition, favouring terrestrial adaptation through enhanced aerial orientation.
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Affiliation(s)
- Demian Burguera
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
| | - Francesco Dionigi
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Kristina Kverková
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Thomas Brown
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Yicheng Zhang
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | | | | | - Eugene Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Pavel Němec
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Zuzana Musilova
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
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3
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O’Leary A, Fernàndez-Castillo N, Gan G, Yang Y, Yotova AY, Kranz TM, Grünewald L, Freudenberg F, Antón-Galindo E, Cabana-Domínguez J, Harneit A, Schweiger JI, Schwarz K, Ma R, Chen J, Schwarz E, Rietschel M, Tost H, Meyer-Lindenberg A, Pané-Farré CA, Kircher T, Hamm AO, Burguera D, Mota NR, Franke B, Schweiger S, Winter J, Heinz A, Erk S, Romanczuk-Seiferth N, Walter H, Ströhle A, Fehm L, Fydrich T, Lueken U, Weber H, Lang T, Gerlach AL, Nöthen MM, Alpers GW, Arolt V, Witt S, Richter J, Straube B, Cormand B, Slattery DA, Reif A. Behavioural and functional evidence revealing the role of RBFOX1 variation in multiple psychiatric disorders and traits. Mol Psychiatry 2022; 27:4464-4473. [PMID: 35948661 PMCID: PMC9734045 DOI: 10.1038/s41380-022-01722-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/16/2022] [Accepted: 07/22/2022] [Indexed: 12/14/2022]
Abstract
Common variation in the gene encoding the neuron-specific RNA splicing factor RNA Binding Fox-1 Homolog 1 (RBFOX1) has been identified as a risk factor for several psychiatric conditions, and rare genetic variants have been found causal for autism spectrum disorder (ASD). Here, we explored the genetic landscape of RBFOX1 more deeply, integrating evidence from existing and new human studies as well as studies in Rbfox1 knockout mice. Mining existing data from large-scale studies of human common genetic variants, we confirmed gene-based and genome-wide association of RBFOX1 with risk tolerance, major depressive disorder and schizophrenia. Data on six mental disorders revealed copy number losses and gains to be more frequent in ASD cases than in controls. Consistently, RBFOX1 expression appeared decreased in post-mortem frontal and temporal cortices of individuals with ASD and prefrontal cortex of individuals with schizophrenia. Brain-functional MRI studies demonstrated that carriers of a common RBFOX1 variant, rs6500744, displayed increased neural reactivity to emotional stimuli, reduced prefrontal processing during cognitive control, and enhanced fear expression after fear conditioning, going along with increased avoidance behaviour. Investigating Rbfox1 neuron-specific knockout mice allowed us to further specify the role of this gene in behaviour. The model was characterised by pronounced hyperactivity, stereotyped behaviour, impairments in fear acquisition and extinction, reduced social interest, and lack of aggression; it provides excellent construct and face validity as an animal model of ASD. In conclusion, convergent translational evidence shows that common variants in RBFOX1 are associated with a broad spectrum of psychiatric traits and disorders, while rare genetic variation seems to expose to early-onset neurodevelopmental psychiatric disorders with and without developmental delay like ASD, in particular. Studying the pleiotropic nature of RBFOX1 can profoundly enhance our understanding of mental disorder vulnerability.
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Affiliation(s)
- Aet O’Leary
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany ,grid.10939.320000 0001 0943 7661Department of Neuropscyhopharmacology, Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Noèlia Fernàndez-Castillo
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, and Institut de Biomedicina de la Universitat de Barcelona (IBUB); Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII); Madrid, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Barcelona, Catalonia Spain
| | - Gabriela Gan
- grid.7700.00000 0001 2190 4373Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Yunbo Yang
- grid.10253.350000 0004 1936 9756Department of Psychiatry and Psychotherapy and Center for Mind, Brain and Behavior - CMBB, University of Marburg, Marburg, Germany
| | - Anna Y. Yotova
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany ,grid.7839.50000 0004 1936 9721Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Thorsten M. Kranz
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Lena Grünewald
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Florian Freudenberg
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ester Antón-Galindo
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, and Institut de Biomedicina de la Universitat de Barcelona (IBUB); Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII); Madrid, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Barcelona, Catalonia Spain
| | - Judit Cabana-Domínguez
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, and Institut de Biomedicina de la Universitat de Barcelona (IBUB); Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII); Madrid, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Barcelona, Catalonia Spain
| | - Anais Harneit
- grid.7700.00000 0001 2190 4373Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Janina I. Schweiger
- grid.7700.00000 0001 2190 4373Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Kristina Schwarz
- grid.7700.00000 0001 2190 4373Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Ren Ma
- grid.7700.00000 0001 2190 4373Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Junfang Chen
- grid.7700.00000 0001 2190 4373Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Emanuel Schwarz
- grid.7700.00000 0001 2190 4373Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Marcella Rietschel
- grid.7700.00000 0001 2190 4373Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Heike Tost
- grid.7700.00000 0001 2190 4373Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Andreas Meyer-Lindenberg
- grid.7700.00000 0001 2190 4373Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Christiane A. Pané-Farré
- grid.10253.350000 0004 1936 9756Department of Psychiatry and Psychotherapy and Center for Mind, Brain and Behavior - CMBB, University of Marburg, Marburg, Germany ,grid.5603.0Department of Biological and Clinical Psychology/Psychotherapy, University of Greifswald, Greifswald, Germany
| | - Tilo Kircher
- grid.10253.350000 0004 1936 9756Department of Psychiatry and Psychotherapy and Center for Mind, Brain and Behavior - CMBB, University of Marburg, Marburg, Germany
| | - Alfons O. Hamm
- grid.5603.0Department of Biological and Clinical Psychology/Psychotherapy, University of Greifswald, Greifswald, Germany
| | - Demian Burguera
- grid.4491.80000 0004 1937 116XDepartment of Zoology, Charles University, Prague, Czech Republic
| | - Nina Roth Mota
- grid.10417.330000 0004 0444 9382Department of Human Genetics and Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Barbara Franke
- grid.10417.330000 0004 0444 9382Department of Human Genetics and Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Susann Schweiger
- grid.10388.320000 0001 2240 3300Mainz University Medical Center, Institute of Human Genetics, Mainz, Germany
| | - Jennifer Winter
- grid.10388.320000 0001 2240 3300Mainz University Medical Center, Institute of Human Genetics, Mainz, Germany
| | - Andreas Heinz
- grid.6363.00000 0001 2218 4662Department of Psychiatry and Psychotherapy, Charité - University Medicine Berlin, Berlin, Germany
| | - Susanne Erk
- grid.6363.00000 0001 2218 4662Department of Psychiatry and Psychotherapy, Charité - University Medicine Berlin, Berlin, Germany
| | - Nina Romanczuk-Seiferth
- grid.6363.00000 0001 2218 4662Department of Psychiatry and Psychotherapy, Charité - University Medicine Berlin, Berlin, Germany
| | - Henrik Walter
- grid.6363.00000 0001 2218 4662Department of Psychiatry and Psychotherapy, Charité - University Medicine Berlin, Berlin, Germany
| | - Andreas Ströhle
- grid.6363.00000 0001 2218 4662Department of Psychiatry and Psychotherapy, Charité - University Medicine Berlin, Berlin, Germany
| | - Lydia Fehm
- grid.7468.d0000 0001 2248 7639Department of Psychology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Thomas Fydrich
- grid.7468.d0000 0001 2248 7639Department of Psychology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ulrike Lueken
- grid.7468.d0000 0001 2248 7639Department of Psychology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Heike Weber
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany ,grid.8379.50000 0001 1958 8658Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Thomas Lang
- grid.15078.3b0000 0000 9397 8745Christoph-Dornier-Foundation for Clinical Psychology, Institute for Clinical Psychology Bremen; Bremen, Germany and Department for Psychology & Methods, Jacobs University Bremen, Bremen, Germany
| | - Alexander L. Gerlach
- grid.6190.e0000 0000 8580 3777Clinical Psychology and Psychotherapy, University of Cologne, Cologne, Germany
| | - Markus M. Nöthen
- grid.10388.320000 0001 2240 3300Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Georg W. Alpers
- grid.5601.20000 0001 0943 599XDepartment of Psychology, School of Social Sciences, University of Mannheim, Mannheim, Germany
| | - Volker Arolt
- grid.5949.10000 0001 2172 9288Department of Psychiatry and Psychotherapy, University of Münster, Münster, Germany
| | - Stephanie Witt
- grid.7700.00000 0001 2190 4373Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Jan Richter
- grid.5603.0Department of Biological and Clinical Psychology/Psychotherapy, University of Greifswald, Greifswald, Germany ,grid.9463.80000 0001 0197 8922Department of Experimental Psychopathology, University of Hildesheim, Hildesheim, Germany
| | - Benjamin Straube
- grid.10253.350000 0004 1936 9756Department of Psychiatry and Psychotherapy and Center for Mind, Brain and Behavior - CMBB, University of Marburg, Marburg, Germany
| | - Bru Cormand
- grid.5841.80000 0004 1937 0247Department de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, and Institut de Biomedicina de la Universitat de Barcelona (IBUB); Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII); Madrid, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Barcelona, Catalonia Spain
| | - David A. Slattery
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andreas Reif
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University Frankfurt, Frankfurt am Main, Germany
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4
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Márquez Y, Mantica F, Cozzuto L, Burguera D, Hermoso-Pulido A, Ponomarenko J, Roy SW, Irimia M. ExOrthist: a tool to infer exon orthologies at any evolutionary distance. Genome Biol 2021; 22:239. [PMID: 34416914 PMCID: PMC8379844 DOI: 10.1186/s13059-021-02441-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. ExOrthist evaluates exon sequence conservation and considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. We demonstrate its use in different evolutionary scenarios: whole genome duplication in frogs and convergence of Nova-regulated splicing networks (https://github.com/biocorecrg/ExOrthist).
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Affiliation(s)
- Yamile Márquez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.
| | - Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Demian Burguera
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Antonio Hermoso-Pulido
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Julia Ponomarenko
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Scott W Roy
- San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain. .,ICREA, Barcelona, Spain.
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5
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Navas-Pérez E, Vicente-García C, Mirra S, Burguera D, Fernàndez-Castillo N, Ferrán JL, López-Mayorga M, Alaiz-Noya M, Suárez-Pereira I, Antón-Galindo E, Ulloa F, Herrera-Úbeda C, Cuscó P, Falcón-Moya R, Rodríguez-Moreno A, D'Aniello S, Cormand B, Marfany G, Soriano E, Carrión ÁM, Carvajal JJ, Garcia-Fernàndez J. Characterization of an eutherian gene cluster generated after transposon domestication identifies Bex3 as relevant for advanced neurological functions. Genome Biol 2020; 21:267. [PMID: 33100228 PMCID: PMC7586669 DOI: 10.1186/s13059-020-02172-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/25/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND One of the most unusual sources of phylogenetically restricted genes is the molecular domestication of transposable elements into a host genome as functional genes. Although these kinds of events are sometimes at the core of key macroevolutionary changes, their origin and organismal function are generally poorly understood. RESULTS Here, we identify several previously unreported transposable element domestication events in the human and mouse genomes. Among them, we find a remarkable molecular domestication that gave rise to a multigenic family in placental mammals, the Bex/Tceal gene cluster. These genes, which act as hub proteins within diverse signaling pathways, have been associated with neurological features of human patients carrying genomic microdeletions in chromosome X. The Bex/Tceal genes display neural-enriched patterns and are differentially expressed in human neurological disorders, such as autism and schizophrenia. Two different murine alleles of the cluster member Bex3 display morphological and physiopathological brain modifications, such as reduced interneuron number and hippocampal electrophysiological imbalance, alterations that translate into distinct behavioral phenotypes. CONCLUSIONS We provide an in-depth understanding of the emergence of a gene cluster that originated by transposon domestication and gene duplication at the origin of placental mammals, an evolutionary process that transformed a non-functional transposon sequence into novel components of the eutherian genome. These genes were integrated into existing signaling pathways involved in the development, maintenance, and function of the CNS in eutherians. At least one of its members, Bex3, is relevant for higher brain functions in placental mammals and may be involved in human neurological disorders.
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Affiliation(s)
- Enrique Navas-Pérez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain
| | - Cristina Vicente-García
- Centro Andaluz de Biología del Desarrollo, CSIC-UPO-JA, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Serena Mirra
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Demian Burguera
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Noèlia Fernàndez-Castillo
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, 08950, Barcelona, Spain
| | - José Luis Ferrán
- Department of Human Anatomy, School of Medicine, University of Murcia and IMIB-Arrixaca Institute, 30120, Murcia, Spain
| | - Macarena López-Mayorga
- Centro Andaluz de Biología del Desarrollo, CSIC-UPO-JA, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Marta Alaiz-Noya
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain.,Present Address: Instituto de Neurociencias de Alicante (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas), Alicante, Spain
| | - Irene Suárez-Pereira
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain.,Present Address: Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Neuropsychopharmacology and psychobiology research group, UCA, INiBICA, Cádiz, Spain
| | - Ester Antón-Galindo
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain
| | - Fausto Ulloa
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain
| | - Carlos Herrera-Úbeda
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain
| | - Pol Cuscó
- Genome Architecture, Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Rafael Falcón-Moya
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Antonio Rodríguez-Moreno
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121, Naples, Italy
| | - Bru Cormand
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, 08950, Barcelona, Spain
| | - Gemma Marfany
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, 08950, Barcelona, Spain
| | - Eduardo Soriano
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III (ISCIII), 28029, Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - Ángel M Carrión
- Department of Physiology, Anatomy and Cell Biology, Universidad Pablo de Olavide, 41013, Sevilla, Spain
| | - Jaime J Carvajal
- Centro Andaluz de Biología del Desarrollo, CSIC-UPO-JA, Universidad Pablo de Olavide, 41013, Sevilla, Spain.
| | - Jordi Garcia-Fernàndez
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, 08028, Barcelona, Spain.
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6
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Adrian-Kalchhauser I, Blomberg A, Larsson T, Musilova Z, Peart CR, Pippel M, Solbakken MH, Suurväli J, Walser JC, Wilson JY, Alm Rosenblad M, Burguera D, Gutnik S, Michiels N, Töpel M, Pankov K, Schloissnig S, Winkler S. The round goby genome provides insights into mechanisms that may facilitate biological invasions. BMC Biol 2020; 18:11. [PMID: 31992286 PMCID: PMC6988351 DOI: 10.1186/s12915-019-0731-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022] Open
Abstract
Background The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success. Results We report a highly contiguous long-read-based genome and analyze gene families that we hypothesize to relate to the ability of these fish to deal with novel environments. The analyses provide novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns of epigenetic regulators, and the presence of osmoregulatory genes that may have contributed to the round goby’s capacity to invade cold and salty waters. A recurring theme across all analyzed gene families is gene expansions. Conclusions The expanded innate immune system of round goby may potentially contribute to its ability to colonize novel areas. Since other gene families also feature copy number expansions in the round goby, and since other Gobiidae also feature fascinating environmental adaptations and are excellent colonizers, further long-read genome approaches across the goby family may reveal whether gene copy number expansions are more generally related to the ability to conquer new habitats in Gobiidae or in fish. Electronic supplementary material The online version of this article (10.1186/s12915-019-0731-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irene Adrian-Kalchhauser
- Program Man-Society-Environment, Department of Environmental Sciences, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland. .,University of Bern, Institute for Fish and Wildlife Health, Länggassstrasse 122, 3012, Bern, Austria.
| | - Anders Blomberg
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Tomas Larsson
- Department of Marine Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Zuzana Musilova
- Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Claire R Peart
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Grosshaderner Strasse 2, 82152 Planegg-, Martinsried, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Monica Hongroe Solbakken
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Blindernveien 31, 0371, Oslo, Norway
| | - Jaanus Suurväli
- Institute for Genetics, University of Cologne, Zülpicher Strasse 47a, 50674, Köln, Germany
| | - Jean-Claude Walser
- Genetic Diversity Centre, ETH, Universitätsstrasse 16, 8092, Zurich, Switzerland
| | - Joanna Yvonne Wilson
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada
| | - Magnus Alm Rosenblad
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden.,NBIS Bioinformatics Infrastructure for Life Sciences, University of Gothenburg, Medicinaregatan 9C, 41390, Gothenburg, Sweden
| | - Demian Burguera
- Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Silvia Gutnik
- Biocenter, University of Basel, Klingelbergstrasse 50/70, 4056, Basel, Switzerland
| | - Nico Michiels
- Institute of Evolution and Ecology, University of Tuebingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Mats Töpel
- University of Bern, Institute for Fish and Wildlife Health, Länggassstrasse 122, 3012, Bern, Austria
| | - Kirill Pankov
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON, Canada
| | - Siegfried Schloissnig
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
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7
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Ramos-Vicente D, Ji J, Gratacòs-Batlle E, Gou G, Reig-Viader R, Luís J, Burguera D, Navas-Perez E, García-Fernández J, Fuentes-Prior P, Escriva H, Roher N, Soto D, Bayés À. Metazoan evolution of glutamate receptors reveals unreported phylogenetic groups and divergent lineage-specific events. eLife 2018; 7:35774. [PMID: 30465522 PMCID: PMC6307864 DOI: 10.7554/elife.35774] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 11/20/2018] [Indexed: 01/28/2023] Open
Abstract
Glutamate receptors are divided in two unrelated families: ionotropic (iGluR), driving synaptic transmission, and metabotropic (mGluR), which modulate synaptic strength. The present classification of GluRs is based on vertebrate proteins and has remained unchanged for over two decades. Here we report an exhaustive phylogenetic study of GluRs in metazoans. Importantly, we demonstrate that GluRs have followed different evolutionary histories in separated animal lineages. Our analysis reveals that the present organization of iGluRs into six classes does not capture the full complexity of their evolution. Instead, we propose an organization into four subfamilies and ten classes, four of which have never been previously described. Furthermore, we report a sister class to mGluR classes I-III, class IV. We show that many unreported proteins are expressed in the nervous system, and that new Epsilon receptors form functional ligand-gated ion channels. We propose an updated classification of glutamate receptors that includes our findings. Nerve cells or neurons communicate with each other by releasing specific molecules in the gap between them, the synapses. The sending neuron passes on messages through packets of chemicals called neurotransmitters, which are picked up by the receiving cell with the help of receptors on its surface. Neurons use different neurotransmitters to send different messages, but one of the most common ones is glutamate. There are two families of glutamate receptors: ionotropic receptors, which can open or close ion channels in response to neurotransmitters and control the transmission of a signal, and metabotropic receptors, which are linked to a specific protein and control the strength of signal. Our understanding of these two receptor families comes from animals with backbones, known as vertebrates. But the receptors themselves are ancient. We can trace the first family back as far as bacteria and the second back to single-celled organisms like amoebas. Vertebrates have six classes of ionotropic and three classes of metabotropic glutamate receptor. But other multi-celled animals also have these receptors, so this picture may not be complete. Here, Ramos-Vicente et al. mapped all major lineages of animals to reveal the evolutionary history of these receptors to find out if the receptor families became more complicated as brain power increased. The results showed that the glutamate receptors found in vertebrates are only a fraction of all the types that exist. In fact, before present-day animal groups emerged, the part of the genome that holds the ionotropic receptor genes duplicated three times. This formed four receptor subfamilies, and our ancestors had all of them. Across the animal kingdom, there are ten, not six, classes of ionotropic receptors and there is an extra class of metabotropic receptors. But only two subfamilies of ionotropic and three out of four metabotropic receptor classes are still present in vertebrates today. The current classification of glutamate receptors centers around vertebrates, ignoring other animals. But this new data could change that. A better knowledge of these new receptors could aid neuroscientists in better understanding the nervous system. And, using this technique to study other families of proteins could reveal more missing links in evolution.
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Affiliation(s)
- David Ramos-Vicente
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jie Ji
- Institute of Biotechnology and Biomedicine, Department of Cell Biology, Animal Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Esther Gratacòs-Batlle
- Neurophysiology Laboratory, Department of Biomedicine, Medical School, August Pi i Sunyer Biomedical Research Institute, Institute of Neurosciences, Universitat de Barcelona, Barcelona, Spain
| | - Gemma Gou
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rita Reig-Viader
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Javier Luís
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Demian Burguera
- Department of Genetics, School of Biology, Institut de Biomedicina, University of Barcelona, Barcelona, Spain
| | - Enrique Navas-Perez
- Department of Genetics, School of Biology, Institut de Biomedicina, University of Barcelona, Barcelona, Spain
| | - Jordi García-Fernández
- Department of Genetics, School of Biology, Institut de Biomedicina, University of Barcelona, Barcelona, Spain
| | - Pablo Fuentes-Prior
- Molecular Bases of Disease, Biomedical Research Institute Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Hector Escriva
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, Banyuls-sur-Mer, France
| | - Nerea Roher
- Institute of Biotechnology and Biomedicine, Department of Cell Biology, Animal Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - David Soto
- Neurophysiology Laboratory, Department of Biomedicine, Medical School, August Pi i Sunyer Biomedical Research Institute, Institute of Neurosciences, Universitat de Barcelona, Barcelona, Spain
| | - Àlex Bayés
- Molecular Physiology of the Synapse Laboratory, Biomedical Research Institute Sant Pau, Barcelona, Spain.,Universitat Autònoma de Barcelona, Barcelona, Spain
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8
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Albuixech-Crespo B, López-Blanch L, Burguera D, Maeso I, Sánchez-Arrones L, Moreno-Bravo JA, Somorjai I, Pascual-Anaya J, Puelles E, Bovolenta P, Garcia-Fernàndez J, Puelles L, Irimia M, Ferran JL. Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain. PLoS Biol 2017; 15:e2001573. [PMID: 28422959 PMCID: PMC5396861 DOI: 10.1371/journal.pbio.2001573] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/22/2017] [Indexed: 11/25/2022] Open
Abstract
All vertebrate brains develop following a common Bauplan defined by anteroposterior (AP) and dorsoventral (DV) subdivisions, characterized by largely conserved differential expression of gene markers. However, it is still unclear how this Bauplan originated during evolution. We studied the relative expression of 48 genes with key roles in vertebrate neural patterning in a representative amphioxus embryonic stage. Unlike nonchordates, amphioxus develops its central nervous system (CNS) from a neural plate that is homologous to that of vertebrates, allowing direct topological comparisons. The resulting genoarchitectonic model revealed that the amphioxus incipient neural tube is unexpectedly complex, consisting of several AP and DV molecular partitions. Strikingly, comparison with vertebrates indicates that the vertebrate thalamus, pretectum, and midbrain domains jointly correspond to a single amphioxus region, which we termed Di-Mesencephalic primordium (DiMes). This suggests that these domains have a common developmental and evolutionary origin, as supported by functional experiments manipulating secondary organizers in zebrafish and mice.
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Affiliation(s)
- Beatriz Albuixech-Crespo
- Department of Genetics, School of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, Barcelona, Spain
| | - Laura López-Blanch
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Demian Burguera
- Department of Genetics, School of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ignacio Maeso
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA), Sevilla, Spain
| | - Luisa Sánchez-Arrones
- Centro de Biología Molecular Severo Ochoa CSIC-UAM and CIBERER, ISCIII, Madrid, Spain
| | | | - Ildiko Somorjai
- The Scottish Oceans Institute, University of St Andrews, St Andrews, Fife, Scotland, United Kingdom
- Biomedical Sciences Research Complex, University of St Andrews, Fife, Scotland, United Kingdom
| | | | - Eduardo Puelles
- Instituto de Neurociencias, UMH-CSIC, Campus de San Juan, Sant Joan d'Alacant, Alicante, Spain
| | - Paola Bovolenta
- Centro de Biología Molecular Severo Ochoa CSIC-UAM and CIBERER, ISCIII, Madrid, Spain
| | - Jordi Garcia-Fernàndez
- Department of Genetics, School of Biology, and Institut de Biomedicina (IBUB), University of Barcelona, Barcelona, Spain
| | - Luis Puelles
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia, Murcia, Spain
- Institute of Biomedical Research of Murcia (IMIB), Virgen de la Arrixaca University Hospital, University of Murcia, Murcia, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - José Luis Ferran
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia, Murcia, Spain
- Institute of Biomedical Research of Murcia (IMIB), Virgen de la Arrixaca University Hospital, University of Murcia, Murcia, Spain
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9
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Abstract
The human CERKL gene is responsible for common and severe forms of retinal dystrophies. Despite intense in vitro studies at the molecular and cellular level and in vivo analyses of the retina of murine knockout models, CERKL function remains unknown. In this study, we aimed to approach the developmental and functional features of cerkl in Danio rerio within an Evo-Devo framework. We show that gene expression increases from early developmental stages until the formation of the retina in the optic cup. Unlike the high mRNA-CERKL isoform multiplicity shown in mammals, the moderate transcriptional complexity in fish facilitates phenotypic studies derived from gene silencing. Moreover, of relevance to pathogenicity, teleost CERKL shares the two main human protein isoforms. Morpholino injection has been used to generate a cerkl knockdown zebrafish model. The morphant phenotype results in abnormal eye development with lamination defects, failure to develop photoreceptor outer segments, increased apoptosis of retinal cells and small eyes. Our data support that zebrafish Cerkl does not interfere with proliferation and neural differentiation during early developmental stages but is relevant for survival and protection of the retinal tissue. Overall, we propose that this zebrafish model is a powerful tool to unveil CERKL contribution to human retinal degeneration.
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Affiliation(s)
- Marina Riera
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
- CIBERER, Instituto de Salud Carlos III, Barcelona, Spain
| | - Demian Burguera
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Jordi Garcia-Fernàndez
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Roser Gonzàlez-Duarte
- Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
- CIBERER, Instituto de Salud Carlos III, Barcelona, Spain
- * E-mail:
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