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Dambroise E, Simion M, Bourquard T, Bouffard S, Rizzi B, Jaszczyszyn Y, Bourge M, Affaticati P, Heuzé A, Jouralet J, Edouard J, Brown S, Thermes C, Poupon A, Reiter E, Sohm F, Bourrat F, Joly JS. Postembryonic Fish Brain Proliferation Zones Exhibit Neuroepithelial-Type Gene Expression Profile. Stem Cells 2017; 35:1505-1518. [PMID: 28181357 DOI: 10.1002/stem.2588] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 01/04/2023]
Abstract
In mammals, neuroepithelial cells play an essential role in embryonic neurogenesis, whereas glial stem cells are the principal source of neurons at postembryonic stages. By contrast, neuroepithelial-like stem/progenitor (NE) cells have been shown to be present throughout life in teleosts. We used three-dimensional (3D) reconstructions of cleared transgenic wdr12:GFP medaka brains to demonstrate that this cell type is widespread in juvenile and to identify new regions containing NE cells. We established the gene expression profile of optic tectum (OT) NE cells by cell sorting followed by RNA-seq. Our results demonstrate that most OT NE cells are indeed active stem cells and that some of them exhibit long G2 phases. We identified several novel pathways (e.g., DNA repair pathways) potentially involved in NE cell homeostasis. In situ hybridization studies showed that all NE populations in the postembryonic medaka brain have a similar molecular signature. Our findings highlight the importance of NE progenitors in medaka and improve our understanding of NE-cell biology. These cells are potentially useful not only for neural stem cell studies but also for improving the characterization of neurodevelopmental diseases, such as microcephaly. Stem Cells 2017;35:1505-1518.
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Affiliation(s)
- Emilie Dambroise
- INRA CASBAH Group, Neuro-PSI, UMR 9197, CNRS, Gif-sur-Yvette, France
| | - Matthieu Simion
- INRA CASBAH Group, Neuro-PSI, UMR 9197, CNRS, Gif-sur-Yvette, France
| | | | | | - Barbara Rizzi
- Tefor Core Facility, TEFOR Infrastructure, Neuro-PSI, CNRS, Gif-sur-Yvette, France
| | | | | | - Pierre Affaticati
- Tefor Core Facility, TEFOR Infrastructure, Neuro-PSI, CNRS, Gif-sur-Yvette, France
| | - Aurélie Heuzé
- INRA CASBAH Group, Neuro-PSI, UMR 9197, CNRS, Gif-sur-Yvette, France
| | - Julia Jouralet
- Plateforme BM-Gif, Imagif, UMR 9198, CNRS, Gif-sur-Yvette, France
| | - Joanne Edouard
- UMS AMAGEN CNRS, INRA, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | | | | | | | - Frédéric Sohm
- UMS AMAGEN CNRS, INRA, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Franck Bourrat
- INRA CASBAH Group, Neuro-PSI, UMR 9197, CNRS, Gif-sur-Yvette, France
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Benítez-Santana T, Simion M, Corraze G, Médale F, Joly JS. Effect of Nutrient Availability on Progenitor Cells in Zebrafish (Danio Rerio). Dev Neurobiol 2016; 77:26-38. [DOI: 10.1002/dneu.22406] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/02/2016] [Accepted: 06/05/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Tibiábin Benítez-Santana
- INRA CASBAH Group, Neuroscience Paris-Saclay Institute (Neuro-PSI) UMR 9197, CNRS - Université Paris Sud; Bat. 32/33, 1 Avenue De La Terrasse Gif-sur-Yvette 91198 France
| | - Matthieu Simion
- INRA CASBAH Group, Neuroscience Paris-Saclay Institute (Neuro-PSI) UMR 9197, CNRS - Université Paris Sud; Bat. 32/33, 1 Avenue De La Terrasse Gif-sur-Yvette 91198 France
| | - Geneviève Corraze
- INRA UR 1067, Nutrition, Metabolism, and Aquaculture; Saint Pée-sur-Nivelle France
| | - Françoise Médale
- INRA UR 1067, Nutrition, Metabolism, and Aquaculture; Saint Pée-sur-Nivelle France
| | - Jean-Stéphane Joly
- INRA CASBAH Group, Neuroscience Paris-Saclay Institute (Neuro-PSI) UMR 9197, CNRS - Université Paris Sud; Bat. 32/33, 1 Avenue De La Terrasse Gif-sur-Yvette 91198 France
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Abstract
The Japanese medaka, Oryzias latipes, is a vertebrate teleost model with a long history of genetic research. A number of unique features and established resources distinguish medaka from other vertebrate model systems. A large number of laboratory strains from different locations are available. Due to a high tolerance to inbreeding, many highly inbred strains have been established, thus providing a rich resource for genetic studies. Furthermore, closely related species native to different habitats in Southeast Asia permit comparative evolutionary studies. The transparency of embryos, larvae, and juveniles allows a detailed in vivo analysis of development. New tools to study diverse aspects of medaka biology are constantly being generated. Thus, medaka has become an important vertebrate model organism to study development, behavior, and physiology. In this review, we provide a comprehensive overview of established genetic and molecular-genetic tools that render medaka fish a full-fledged vertebrate system.
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Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle. PLoS One 2015; 10:e0141487. [PMID: 26505748 PMCID: PMC4624239 DOI: 10.1371/journal.pone.0141487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/08/2015] [Indexed: 01/01/2023] Open
Abstract
Enhancers have been described to evolve by permutation without changing function. This has posed the problem of how to predict enhancer elements that are hidden from alignment-based approaches due to the loss of co-linearity. Alignment-free algorithms have been proposed as one possible solution. However, this approach is hampered by several problems inherent to its underlying working principle. Here we present a new approach, which combines the power of alignment and alignment-free techniques into one algorithm. It allows the prediction of enhancers based on the query and target sequence only, no matter whether the regulatory logic is co-linear or reshuffled. To test our novel approach, we employ it for the prediction of enhancers across the evolutionary distance of ~450Myr between human and medaka. We demonstrate its efficacy by subsequent in vivo validation resulting in 82% (9/11) of the predicted medaka regions showing reporter activity. These include five candidates with partially co-linear and four with reshuffled motif patterns. Orthology in flanking genes and conservation of the detected co-linear motifs indicates that those candidates are likely functionally equivalent enhancers. In sum, our results demonstrate that the proposed principle successfully predicts mutated as well as permuted enhancer regions at an encouragingly high rate.
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Alonso-Barba JI, Rahman RU, Wittbrodt J, Mateo JL. MEPD: medaka expression pattern database, genes and more. Nucleic Acids Res 2015; 44:D819-21. [PMID: 26450962 PMCID: PMC4702773 DOI: 10.1093/nar/gkv1029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
The Medaka Expression Pattern Database (MEPD; http://mepd.cos.uni-heidelberg.de/) is designed as a repository of medaka expression data for the scientific community. In this update we present two main improvements. First, we have changed the previous clone-centric view for in situ data to a gene-centric view. This is possible because now we have linked all the data present in MEPD to the medaka gene annotation in ENSEMBL. In addition, we have also connected the medaka genes in MEPD to their corresponding orthologous gene in zebrafish, again using the ENSEMBL database. Based on this, we provide a link to the Zebrafish Model Organism Database (ZFIN) to allow researches to compare expression data between these two fish model organisms. As a second major improvement, we have modified the design of the database to enable it to host regulatory elements, promoters or enhancers, expression patterns in addition to gene expression. The combination of gene expression, by traditional in situ, and regulatory element expression, typically by fluorescence reporter gene, within the same platform assures consistency in terms of annotation. In our opinion, this will allow researchers to uncover new insights between the expression domain of genes and their regulatory landscape.
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Affiliation(s)
- Juan I Alonso-Barba
- Department of Computing Systems, University of Castilla-La Mancha, Albacete, 02071, Spain
| | - Raza-Ur Rahman
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Juan L Mateo
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
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Backfisch B, Kozin VV, Kirchmaier S, Tessmar-Raible K, Raible F. Tools for gene-regulatory analyses in the marine annelid Platynereis dumerilii. PLoS One 2014; 9:e93076. [PMID: 24714200 PMCID: PMC3979674 DOI: 10.1371/journal.pone.0093076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 03/03/2014] [Indexed: 01/22/2023] Open
Abstract
The advent of high-throughput sequencing technology facilitates the exploration of a variety of reference species outside the few established molecular genetic model systems. Bioinformatic and gene expression analyses provide new ways for comparative analyses between species, for instance, in the field of evolution and development. Despite these advances, a critical bottleneck for the exploration of new model species remains the establishment of functional tools, such as the ability to experimentally express genes in specific cells of an organism. We recently established a first transgenic strain of the annelid Platynereis, using a Tc1/mariner-type Mos1 transposon vector. Here, we compare Mos1 with Tol2, a member of the hAT family of transposons. In Platynereis, Tol2-based constructs showed a higher frequency of nuclear genome insertion and sustained gene expression in the G0 generation. However, in contrast to Mos1-mediated transgenes, Tol2-mediated insertions failed to retain fluorescence in the G1 generation, suggesting a germ line-based silencing mechanism. Furthermore, we present three novel expression constructs that were generated by a simple fusion-PCR approach and allow either ubiquitous or cell-specific expression of a reporter gene. Our study indicates the versatility of Tol2 for transient transgenesis, and provides a template for transgenesis work in other emerging reference species.
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Affiliation(s)
- Benjamin Backfisch
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
- Research Platform “Marine Rhythms of Life,” University of Vienna, Vienna, Austria
| | - Vitaly V. Kozin
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
- Department of Embryology, St. Petersburg State University, St. Petersburg, Russia
| | - Stephan Kirchmaier
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
- Research Platform “Marine Rhythms of Life,” University of Vienna, Vienna, Austria
| | - Florian Raible
- Max Ferdinand Perutz Laboratories (MFPL), University of Vienna, Vienna, Austria
- Research Platform “Marine Rhythms of Life,” University of Vienna, Vienna, Austria
- * E-mail:
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Genomic and phenotypic characterization of a wild medaka population: towards the establishment of an isogenic population genetic resource in fish. G3-GENES GENOMES GENETICS 2014; 4:433-45. [PMID: 24408034 PMCID: PMC3962483 DOI: 10.1534/g3.113.008722] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Oryzias latipes (medaka) has been established as a vertebrate genetic model for more than a century and recently has been rediscovered outside its native Japan. The power of new sequencing methods now makes it possible to reinvigorate medaka genetics, in particular by establishing a near-isogenic panel derived from a single wild population. Here we characterize the genomes of wild medaka catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of a near-isogenic panel of wild lines. The population is free of significant detrimental population structure and has advantageous linkage disequilibrium properties suitable for the establishment of the proposed panel. Analysis of morphometric traits in five representative inbred strains suggests phenotypic mapping will be feasible in the panel. In addition, high-throughput genome sequencing of these medaka strains confirms their evolutionary relationships on lines of geographic separation and provides further evidence that there has been little significant interbreeding between the Southern and Northern medaka population since the Southern/Northern population split. The sequence data suggest that the Southern Japanese medaka existed as a larger older population that went through a relatively recent bottleneck approximately 10,000 years ago. In addition, we detect patterns of recent positive selection in the Southern population. These data indicate that the genetic structure of the Kiyosu medaka samples is suitable for the establishment of a vertebrate near-isogenic panel and therefore inbreeding of 200 lines based on this population has commenced. Progress of this project can be tracked at http://www.ebi.ac.uk/birney-srv/medaka-ref-panel.
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Kirchmaier S, Höckendorf B, Möller EK, Bornhorst D, Spitz F, Wittbrodt J. Efficient site-specific transgenesis and enhancer activity tests in medaka using PhiC31 integrase. Development 2013; 140:4287-95. [PMID: 24048591 PMCID: PMC3809364 DOI: 10.1242/dev.096081] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Established transgenesis methods for fish model systems allow efficient genomic integration of transgenes. However, thus far a way of controlling copy number and integration sites has not been available, leading to variable transgene expression caused by position effects. The integration of transgenes at predefined genomic positions enables the direct comparison of different transgenes, thereby improving time and cost efficiency. Here, we report an efficient PhiC31-based site-specific transgenesis system for medaka. This system includes features that allow the pre-selection of successfully targeted integrations early on in the injected generation. Pre-selected embryos transmit the correctly integrated transgene through the germline with high efficiency. The landing site design enables a variety of applications, such as reporter and enhancer switch, in addition to the integration of any insert. Importantly, this allows assaying of enhancer activity in a site-specific manner without requiring germline transmission, thus speeding up large-scale analyses of regulatory elements.
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Affiliation(s)
- Stephan Kirchmaier
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
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A novel mammal-specific three partite enhancer element regulates node and notochord-specific Noto expression. PLoS One 2012; 7:e47785. [PMID: 23110100 PMCID: PMC3478275 DOI: 10.1371/journal.pone.0047785] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 09/17/2012] [Indexed: 11/19/2022] Open
Abstract
The vertebrate organizer and notochord have conserved, essential functions for embryonic development and patterning. The restricted expression of developmental regulators in these tissues is directed by specific cis-regulatory modules (CRMs) whose sequence conservation varies considerably. Some CRMs have been conserved throughout vertebrates and likely represent ancestral regulatory networks, while others have diverged beyond recognition but still function over a wide evolutionary range. Here we identify and characterize a mammalian-specific CRM required for node and notochord specific (NNC) expression of NOTO, a transcription factor essential for node morphogenesis, nodal cilia movement and establishment of laterality in mouse. A 523 bp enhancer region (NOCE) upstream the Noto promoter was necessary and sufficient for NNC expression from the endogenous Noto locus. Three subregions in NOCE together mediated full activity in vivo. Binding sites for known transcription factors in NOCE were functional in vitro but dispensable for NOCE activity in vivo. A FOXA2 site in combination with a novel motif was necessary for NOCE activity in vivo. Strikingly, syntenic regions in non-mammalian vertebrates showed no recognizable sequence similarities. In contrast to its activity in mouse NOCE did not drive NNC expression in transgenic fish. NOCE represents a novel, mammal-specific CRM required for the highly restricted Noto expression in the node and nascent notochord and thus regulates normal node development and function.
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Eichenlaub MP, Ettwiller L. De novo genesis of enhancers in vertebrates. PLoS Biol 2011; 9:e1001188. [PMID: 22069375 PMCID: PMC3206014 DOI: 10.1371/journal.pbio.1001188] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 09/22/2011] [Indexed: 02/02/2023] Open
Abstract
Whole genome duplication in teleost fish reveals that a few changes in non-regulatory genomic sequences are a source for generating new enhancers. Evolutionary innovation relies partially on changes in gene regulation. While a growing body of evidence demonstrates that such innovation is generated by functional changes or translocation of regulatory elements via mobile genetic elements, the de novo generation of enhancers from non-regulatory/non-mobile sequences has, to our knowledge, not previously been demonstrated. Here we show evidence for the de novo genesis of enhancers in vertebrates. For this, we took advantage of the massive gene loss following the last whole genome duplication in teleosts to systematically identify regions that have lost their coding capacity but retain sequence conservation with mammals. We found that these regions show enhancer activity while the orthologous coding regions have no regulatory activity. These results demonstrate that these enhancers have been de novo generated in fish. By revealing that minor changes in non-regulatory sequences are sufficient to generate new enhancers, our study highlights an important playground for creating new regulatory variability and evolutionary innovation. The genome of each living organism contains thousands of genes, and the precise control of the timing and location of expression of these genes is key for normal development and homeostasis of each individual. Despite the oftentimes high genetic similarity between organisms, the source of phenotypic differences, for example between human and mouse, is thought to originate mainly from changes in how and when genes are expressed. This is partially determined by enhancers, that contribute to the control of gene expression. For decades, duplication of existing genomic enhancers, mobile elements, and changes in the sequence of existing enhancers were believed to be the major ways of increasing the number and modifying the activity of enhancers. In this study, we show that enhancers don't have to be derived from pre-existing ones but can also appear de novo in regions of the genome that were previously not regulating gene expression. We analyzed teleost fish genomes and found three regions for which a limited number of changes in the DNA sequence was sufficient to generate new enhancers. We predict that such a process is frequent in vertebrate genomes, making de novo generation of enhancers an important mechanism for creating variation in gene expression.
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Affiliation(s)
| | - Laurence Ettwiller
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
- * E-mail:
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Smith JJ, Sumiyama K, Amemiya CT. A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome. Mol Biol Evol 2011; 29:985-93. [PMID: 22045999 DOI: 10.1093/molbev/msr267] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Emerging data from the coelacanth genome are beginning to shed light on the origin and evolution of tetrapod genes and noncoding elements. Of particular relevance is the realization that coelacanth retains active copies of transposable elements that once served as raw material for the evolution of new functional sequences in the vertebrate lineage. Recognizing the evolutionary significance of coelacanth genome in this regard, we employed an ab initio search strategy to further classify its repetitive complement. This analysis uncovered a class of interspersed elements (Latimeria Harbinger 1-LatiHarb1) that is a major contributor to coelacanth genome structure and gene content (∼1% to 4% or the genome). Sequence analyses indicate that 1) each ∼8.7 kb LatiHarb1 element contains two coding regions, a transposase gene and a gene whose function is as yet unknown (MYB-like) and 2) copies of LatiHarb1 retain biological activity in the coelacanth genome. Functional analyses verify transcriptional and enhancer activities of LatiHarb1 in vivo and reveal transcriptional decoupling that could permit MYB-like genes to play functional roles not directly linked to transposition. Thus, LatiHarb1 represents the first known instance of a harbinger-superfamily transposon with contemporary activity in a vertebrate genome. Analyses of LatiHarb1 further corroborate the notion that exaptation of anciently active harbinger elements gave rise to at least two vertebrate genes (harbi1 and naif1) and indicate that the vertebrate gene tsnare1 also traces its ancestry to this transposon superfamily. Based on our analyses of LatiHarb1, we speculate that several functional features of harbinger elements may predispose the transposon superfamily toward recurrent exaptive evolution of cellular coding genes. In addition, these analyses further reinforce the broad utility of the coelacanth genome and other "outgroup" genomes in understanding the ancestry and evolution of vertebrate genes and genomes.
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Affiliation(s)
- Jeramiah J Smith
- Benaroya Research Institute at Virginia Mason Medical Center, Seattle, WA, USA.
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