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Waples RS, Elz A, Arnsberg BD, Faulkner JR, Hard JJ, Timmins-Schiffman E, Park LK. Human-mediated evolution in a threatened species? Juvenile life-history changes in Snake River salmon. Evol Appl 2017; 10:667-681. [PMID: 28717387 PMCID: PMC5511361 DOI: 10.1111/eva.12468] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 02/10/2017] [Indexed: 01/21/2023] Open
Abstract
Evaluations of human impacts on Earth's ecosystems often ignore evolutionary changes in response to altered selective regimes. Freshwater habitats for Snake River fall Chinook salmon (SRFCS), a threatened species in the US, have been dramatically changed by hydropower development and other watershed modifications. Associated biological changes include a shift in juvenile life history: Historically essentially 100% of juveniles migrated to sea as subyearlings, but a substantial fraction have migrated as yearlings in recent years. In contemplating future management actions for this species should major Snake River dams ever be removed (as many have proposed), it will be important to understand whether evolution is at least partially responsible for this life-history change. We hypothesized that if this trait is genetically based, parents who migrated to sea as subyearlings should produce faster-growing offspring that would be more likely to reach a size threshold to migrate to sea in their first year. We tested this with phenotypic data for over 2,600 juvenile SRFCS that were genetically matched to parents of hatchery and natural origin. Three lines of evidence supported our hypothesis: (i) the animal model estimated substantial heritability for juvenile growth rate for three consecutive cohorts; (ii) linear modeling showed an association between juvenile life history of parents and offspring growth rate; and (iii) faster-growing juveniles migrated at greater speeds, as expected if they were more likely to be heading to sea. Surprisingly, we also found that parents reared a full year in a hatchery produced the fastest growing offspring of all-apparently an example of cross-generational plasticity associated with artificial propagation. We suggest that SRFCS is an example of a potentially large class of species that can be considered to be "anthro-evolutionary"-signifying those whose evolutionary trajectories have been profoundly shaped by altered selective regimes in human-dominated landscapes.
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Affiliation(s)
- Robin S Waples
- Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Seattle WA USA
| | - Anna Elz
- Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Seattle WA USA
| | - Billy D Arnsberg
- Department of Fisheries Resources Management Nez Perce Tribe Lapwai ID USA
| | - James R Faulkner
- Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Seattle WA USA
| | - Jeffrey J Hard
- Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Seattle WA USA
| | - Emma Timmins-Schiffman
- Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Seattle WA USA.,Department of Genome Sciences University of Washington Seattle WA USA
| | - Linda K Park
- Northwest Fisheries Science Center National Marine Fisheries Service National Oceanic and Atmospheric Administration Seattle WA USA
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Miccoli A, Dalla Valle L, Carnevali O. The maternal control in the embryonic development of zebrafish. Gen Comp Endocrinol 2017; 245:55-68. [PMID: 27013380 DOI: 10.1016/j.ygcen.2016.03.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/16/2016] [Accepted: 03/19/2016] [Indexed: 12/13/2022]
Abstract
The maternal control directing the very first hours of life is of pivotal importance for ensuring proper development to the growing embryo. Thanks to the finely regulated inheritance of maternal factors including mRNAs and proteins produced during oogenesis and stored into the mature oocyte, the embryo is sustained throughout the so-called maternal-to-zygotic transition, a period in development characterized by a species-specific length in time, during which critical biological changes regarding cell cycle and zygotic transcriptional activation occur. In order not to provoke any kind of persistent damage, the process must be delicately balanced. Surprisingly, our knowledge as to the possible effects of beneficial bacteria regarding the modulation of the quality and/or quantity of both maternally-supplied and zygotically-transcribed mRNAs, is very limited. To date, only one group has investigated the consequences of the parentally-supplied Lactobacillus rhamnosus on the storage of mRNAs into mature oocytes, leading to an altered maternal control process in the F1 generation. Particular attention was called on the monitoring of several biomarkers involved in autophagy, apoptosis and axis patterning, while data on miRNA generation and pluripotency maintenance are herein presented for the first time, and can assist in laying the ground for further investigations in this field. In this review, the reader is supplied with the current knowledge on the above-mentioned biological process, first by drawing the general background and then by emphasizing the most important findings that have highlighted their focal role in normal animal development.
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Affiliation(s)
- Andrea Miccoli
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | | | - Oliana Carnevali
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy.
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Romney AL, Podrabsky JE. Transcriptomic analysis of maternally provisioned cues for phenotypic plasticity in the annual killifish, Austrofundulus limnaeus. EvoDevo 2017; 8:6. [PMID: 28439397 PMCID: PMC5401559 DOI: 10.1186/s13227-017-0069-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/14/2017] [Indexed: 12/20/2022] Open
Abstract
Background Genotype and environment can interact during development to produce novel adaptive traits that support life in extreme conditions. The development of the annual killifish Austrofundulus limnaeus is unique among vertebrates because the embryos have distinct cell movements that separate epiboly from axis formation during early development, can enter into a state of metabolic dormancy known as diapause and can survive extreme environmental conditions. The ability to enter into diapause can be maternally programmed, with young females producing embryos that do not enter into diapause. Alternately, embryos can be programmed to “escape” from diapause and develop directly by both maternal factors and embryonic incubation conditions. Thus, maternally packaged gene products are hypothesized to regulate developmental trajectory and perhaps the other unique developmental characters in this species. Results Using high-throughput RNA sequencing, we generated transcriptomic profiles of mRNAs, long non-coding RNAs and small non-coding RNAs (sncRNAs) in 1–2 cell stage embryos of A. limnaeus. Transcriptomic analyses suggest maternal programming of embryos through alternatively spliced mRNAs and antisense sncRNAs. Comparison of these results to those of comparable studies on zebrafish and other fishes reveals a surprisingly high abundance of transcripts involved in the cellular response to stress and a relatively lower expression of genes required for rapid transition through the cell cycle. Conclusions Maternal programming of developmental trajectory is unlikely accomplished by differential expression of diapause-specific genes. Rather, evidence suggests a role for trajectory-specific splice variants of genes expressed in both phenotypes. In addition, based on comparative studies with zebrafish, the A. limnaeus 1–2 cell stage transcriptome is unique in ways that are consistent with their unique life history. These results not only impact our understanding of the genetic mechanisms that regulate entrance into diapause, but also provide insight into the epigenetic regulation of gene expression during development. Electronic supplementary material The online version of this article (doi:10.1186/s13227-017-0069-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amie L Romney
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207 USA
| | - Jason E Podrabsky
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207 USA
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Palomino J, Herrera G, Torres-Fuentes J, Dettleff P, Patel A, Martínez V. Assessment of cathepsin mRNA expression and enzymatic activity during early embryonic development in the yellowtail kingfish Seriola lalandi. Anim Reprod Sci 2017; 180:23-29. [PMID: 28262464 DOI: 10.1016/j.anireprosci.2017.02.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 01/09/2017] [Accepted: 02/19/2017] [Indexed: 12/14/2022]
Abstract
In pelagic species such as Seriola lalandi, survival of both the eggs and embryos depends on yolk processing during oocyte maturation and embryo development. The main enzymes involved in these processes are the cathepsins, which are essential for the hydration process, acquiring buoyancy and nutrition of the embryo before hatching. This study aimed to investigate the mRNA expression profiles of cathepsins B, D and L (catb, catd and catl) and the activity of these enzymes during early development in S. lalandi. We included previtellogenic oocytes (PO). All three enzymes were highly expressed in PO, but the expression was reduced throughout development. Between PO and recently spawned eggs (E1) the transcript to catb and catd decreased, unlike catl. Cathepsin B activity, showed stable levels between PO until blastula stage (E4). High activities levels of cathepsins D and L were observed in E1 in comparison with later developmental stages. Cathepsin L activity remained constant until E1, consistent with observations in other pelagic spawners, where its participation in a second protolithic cleavage of the yolk proteins, has been proposed for this enzyme. Their profiles of both mRNA expression and enzymatic activity indicate the importance of these enzymes during early development and suggest different roles in egg yolk processing for the hydration process and nutrition in early embryos in this species.
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Affiliation(s)
- Jaime Palomino
- FAVET-INBIOGEN, Faculty of Veterinary Sciences, University of Chile, Avda. Santa Rosa 11735, Casilla 2 Correo 15, Santiago, Chile; Animal Reproduction Laboratory, Faculty of Veterinary Sciences, University of Chile, Avda. Santa Rosa 11735, Casilla 2 Correo 15, Santiago, Chile
| | - Giannina Herrera
- FAVET-INBIOGEN, Faculty of Veterinary Sciences, University of Chile, Avda. Santa Rosa 11735, Casilla 2 Correo 15, Santiago, Chile; Animal Reproduction Laboratory, Faculty of Veterinary Sciences, University of Chile, Avda. Santa Rosa 11735, Casilla 2 Correo 15, Santiago, Chile
| | - Jorge Torres-Fuentes
- Animal Reproduction Laboratory, Faculty of Veterinary Sciences, University of Chile, Avda. Santa Rosa 11735, Casilla 2 Correo 15, Santiago, Chile
| | - Phillip Dettleff
- FAVET-INBIOGEN, Faculty of Veterinary Sciences, University of Chile, Avda. Santa Rosa 11735, Casilla 2 Correo 15, Santiago, Chile
| | - Alok Patel
- FAVET-INBIOGEN, Faculty of Veterinary Sciences, University of Chile, Avda. Santa Rosa 11735, Casilla 2 Correo 15, Santiago, Chile
| | - Víctor Martínez
- FAVET-INBIOGEN, Faculty of Veterinary Sciences, University of Chile, Avda. Santa Rosa 11735, Casilla 2 Correo 15, Santiago, Chile.
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Svoboda P, Fulka H, Malik R. Clearance of Parental Products. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 953:489-535. [DOI: 10.1007/978-3-319-46095-6_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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The Tetraodon nigroviridis reference transcriptome: developmental transition, length retention and microsynteny of long non-coding RNAs in a compact vertebrate genome. Sci Rep 2016; 6:33210. [PMID: 27628538 PMCID: PMC5024134 DOI: 10.1038/srep33210] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/28/2016] [Indexed: 01/03/2023] Open
Abstract
Pufferfish such as fugu and tetraodon carry the smallest genomes among all vertebrates and are ideal for studying genome evolution. However, comparative genomics using these species is hindered by the poor annotation of their genomes. We performed RNA sequencing during key stages of maternal to zygotic transition of Tetraodon nigroviridis and report its first developmental transcriptome. We assembled 61,033 transcripts (23,837 loci) representing 80% of the annotated gene models and 3816 novel coding transcripts from 2667 loci. We demonstrate the similarities of gene expression profiles between pufferfish and zebrafish during maternal to zygotic transition and annotated 1120 long non-coding RNAs (lncRNAs) many of which differentially expressed during development. The promoters for 60% of the assembled transcripts result validated by CAGE-seq. Despite the extreme compaction of the tetraodon genome and the dramatic loss of transposons, the length of lncRNA exons remain comparable to that of other vertebrates and a small set of lncRNAs appears enriched for transposable elements suggesting a selective pressure acting on lncRNAs length and composition. Finally, a set of lncRNAs are microsyntenic between teleost and vertebrates, which indicates potential regulatory interactions between lncRNAs and their flanking coding genes. Our work provides a fundamental molecular resource for vertebrate comparative genomics and embryogenesis studies.
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Dupret B, Völkel P, Le Bourhis X, Angrand PO. The Polycomb Group Protein Pcgf1 Is Dispensable in Zebrafish but Involved in Early Growth and Aging. PLoS One 2016; 11:e0158700. [PMID: 27442247 PMCID: PMC4956247 DOI: 10.1371/journal.pone.0158700] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/19/2016] [Indexed: 12/31/2022] Open
Abstract
Polycomb Repressive Complex (PRC) 1 regulates the control of gene expression programs via chromatin structure reorganization. Through mutual exclusion, different PCGF members generate a variety of PRC1 complexes with potentially distinct cellular functions. In this context, the molecular function of each of the PCGF family members remains elusive. The study of PCGF family member expression in zebrafish development and during caudal fin regeneration reveals that the zebrafish pcgf genes are subjected to different regulations and that all PRC1 complexes in terms of Pcgf subunit composition are not always present in the same tissues. To unveil the function of Pcgf1 in zebrafish, a mutant line was generated using the TALEN technology. Mutant pcgf1-/- fish are viable and fertile, but the growth rate at early developmental stages is reduced in absence of pcgf1 gene function and a significant number of pcgf1-/- fish show signs of premature aging. This first vertebrate model lacking Pcgf1 function shows that this Polycomb Group protein is involved in cell proliferation during early embryogenesis and establishes a link between epigenetics and aging.
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Affiliation(s)
- Barbara Dupret
- Cell Plasticity & Cancer, Inserm U908 / University of Lille, Lille, France
| | - Pamela Völkel
- Cell Plasticity & Cancer, Inserm U908 / University of Lille, Lille, France
- CNRS, Lille, France
| | - Xuefen Le Bourhis
- Cell Plasticity & Cancer, Inserm U908 / University of Lille, Lille, France
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58
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Hand SC, Denlinger DL, Podrabsky JE, Roy R. Mechanisms of animal diapause: recent developments from nematodes, crustaceans, insects, and fish. Am J Physiol Regul Integr Comp Physiol 2016; 310:R1193-211. [PMID: 27053646 PMCID: PMC4935499 DOI: 10.1152/ajpregu.00250.2015] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 03/11/2016] [Indexed: 01/22/2023]
Abstract
Life cycle delays are beneficial for opportunistic species encountering suboptimal environments. Many animals display a programmed arrest of development (diapause) at some stage(s) of their development, and the diapause state may or may not be associated with some degree of metabolic depression. In this review, we will evaluate current advancements in our understanding of the mechanisms responsible for the remarkable phenotype, as well as environmental cues that signal entry and termination of the state. The developmental stage at which diapause occurs dictates and constrains the mechanisms governing diapause. Considerable progress has been made in clarifying proximal mechanisms of metabolic arrest and the signaling pathways like insulin/Foxo that control gene expression patterns. Overlapping themes are also seen in mechanisms that control cell cycle arrest. Evidence is emerging for epigenetic contributions to diapause regulation via small RNAs in nematodes, crustaceans, insects, and fish. Knockdown of circadian clock genes in selected insect species supports the importance of clock genes in the photoperiodic response that cues diapause. A large suite of chaperone-like proteins, expressed during diapause, protects biological structures during long periods of energy-limited stasis. More information is needed to paint a complete picture of how environmental cues are coupled to the signal transduction that initiates the complex diapause phenotype, as well as molecular explanations for how the state is terminated. Excellent examples of molecular memory in post-dauer animals have been documented in Caenorhabditis elegans It is clear that a single suite of mechanisms does not regulate diapause across all species and developmental stages.
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Affiliation(s)
- Steven C Hand
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana;
| | - David L Denlinger
- Departments of Entomology and Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, Ohio
| | - Jason E Podrabsky
- Department of Biology, Portland State University, Portland, Oregon; and
| | - Richard Roy
- Department of Biology, McGill University, Montréal, Québec, Canada
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Oda-Ishii I, Kubo A, Kari W, Suzuki N, Rothbächer U, Satou Y. A Maternal System Initiating the Zygotic Developmental Program through Combinatorial Repression in the Ascidian Embryo. PLoS Genet 2016; 12:e1006045. [PMID: 27152625 PMCID: PMC4859511 DOI: 10.1371/journal.pgen.1006045] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 04/20/2016] [Indexed: 01/28/2023] Open
Abstract
Maternal factors initiate the zygotic developmental program in animal embryos. In embryos of the chordate, Ciona intestinalis, three maternal factors—Gata.a, β-catenin, and Zic-r.a—are required to establish three domains of gene expression at the 16-cell stage; the animal hemisphere, vegetal hemisphere, and posterior vegetal domains. Here, we show how the maternal factors establish these domains. First, only β-catenin and its effector transcription factor, Tcf7, are required to establish the vegetal hemisphere domain. Second, genes specifically expressed in the posterior vegetal domain have additional repressive cis-elements that antagonize the activity of β-catenin/Tcf7. This antagonizing activity is suppressed by Zic-r.a, which is specifically localized in the posterior vegetal domain and binds to DNA indirectly through the interaction with Tcf7. Third, Gata.a directs specific gene expression in the animal hemisphere domain, because β-catenin/Tcf7 weakens the Gata.a-binding activity for target sites through a physical interaction in the vegetal cells. Thus, repressive regulation through protein-protein interactions among the maternal transcription factors is essential to establish the first distinct domains of gene expression in the chordate embryo. During animal development, transcription factors and signaling molecules transcriptionally regulate one another and constitute a gene regulatory network. This network is evoked by maternally provided factors. Many maternal factors are localized and thereby activate a set of genes in a specific region. In embryos of the chordate, Ciona intestinalis, three maternal factors with localized activities are known. The present study demonstrated that these localized maternal factors interact with one another through a fourth non-localized transcription factor, Tcf7, and negatively regulate one another. These repressive interactions are essential to establish the first distinct domains of gene expression and evoke the gene regulatory network properly. The findings indicate that not only activating target genes but also repressing activities of other transcription factors through protein-protein interactions are important to properly initiate the zygotic program. Intriguingly, in one repressive interaction, a transcription factor loses its binding activity for target sites through an interaction with another transcription factor. Thus, this study provides a description of the entire system in which maternal factors initiate the zygotic developmental program of the Ciona embryo.
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Affiliation(s)
- Izumi Oda-Ishii
- Department of Zoology, Graduate School of Science, Kyoto University, Kita-Shirakawa Oiwake-cho, Sakyo, Kyoto, Japan
| | - Atsushi Kubo
- Department of Zoology, Graduate School of Science, Kyoto University, Kita-Shirakawa Oiwake-cho, Sakyo, Kyoto, Japan
| | - Willi Kari
- Department of Evolution and Developmental Biology, Zoological Institute, University Innsbruck, Innsbruck, Austria
| | - Nobuhiro Suzuki
- Department of Zoology, Graduate School of Science, Kyoto University, Kita-Shirakawa Oiwake-cho, Sakyo, Kyoto, Japan
| | - Ute Rothbächer
- Department of Evolution and Developmental Biology, Zoological Institute, University Innsbruck, Innsbruck, Austria
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kita-Shirakawa Oiwake-cho, Sakyo, Kyoto, Japan
- * E-mail:
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60
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Michalik O, Kowalski RK, Judycka S, Rożyński R, Dobosz S, Ocalewicz K. Androgenetic development of X- and Y-chromosome bearing haploid rainbow trout embryos. Theriogenology 2016; 86:1054-1060.e1. [PMID: 27125692 DOI: 10.1016/j.theriogenology.2016.03.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 03/21/2016] [Accepted: 03/21/2016] [Indexed: 02/01/2023]
Abstract
Haploid fish embryos are important in studies regarding role of the recessive traits during early ontogeny. In fish species with the male heterogamety, androgenetic haploid embryos might be also useful tool in studies concerning role of the sex chromosomes during an embryonic development. Morphologically differentiated X and Y chromosomes have been found in a limited number of fish species including rainbow trout (Oncorhynchus mykiss Walbaum 1792). To evaluate role of the sex chromosomes during rainbow trout embryonic development, survival of the androgenetic haploids in the presence of X or Y sex chromosomes has been examined. Androgenetic haploid rainbow trout were produced by fertilization of X-irradiated eggs with spermatozoa derived from the normal males (XY) and neomales, that is, sex-reversed females (XX) to produce X- and Y-bearing haploids, and all X-bearing haploids, respectively. Survival rates of the androgenetic progenies of normal males and neomales examined during embryogenesis and at hatching did not differ significantly. However, all haploids died within next few days after hatching. Cytogenetic analysis of the androgenetic embryos confirmed their haploid status. Moreover, apart from the intact paternal chromosomes, residues of the irradiated maternal chromosomes observed as chromosome fragments were identified in some of the haploids. Provided results suggested that rainbow trout X and Y chromosomes despite morphological and genetic differences are at the early stage of differentiation and still share genetic information responsible for the proper embryonic development.
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Affiliation(s)
- Oliwia Michalik
- Department of Molecular Evolution, University of Gdansk, ul. Wita Stwosza 59, 80-308 Gdansk, Poland
| | - Radosław K Kowalski
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, 10-748 Olsztyn, Poland
| | - Sylwia Judycka
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, 10-748 Olsztyn, Poland
| | - Rafał Rożyński
- Department of Salmonid Research, Inland Fisheries Institute in Olsztyn, Rutki, 83-330 Zukowo, Poland
| | - Stefan Dobosz
- Department of Salmonid Research, Inland Fisheries Institute in Olsztyn, Rutki, 83-330 Zukowo, Poland
| | - Konrad Ocalewicz
- Department of Marine Biology and Ecology, Institute of Oceanography, University of Gdansk, Al. M. Piłsudskiego 46, 81-378 Gdynia, Poland.
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61
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Bragato C, Gaudenzi G, Blasevich F, Pavesi G, Maggi L, Giunta M, Cotelli F, Mora M. Zebrafish as a Model to Investigate Dynamin 2-Related Diseases. Sci Rep 2016; 6:20466. [PMID: 26842864 PMCID: PMC4740890 DOI: 10.1038/srep20466] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 01/05/2016] [Indexed: 12/13/2022] Open
Abstract
Mutations in the dynamin-2 gene (DNM2) cause autosomal dominant centronuclear myopathy (CNM) and dominant intermediate Charcot-Marie-Tooth (CMT) neuropathy type B (CMTDIB). As the relation between these DNM2-related diseases is poorly understood, we used zebrafish to investigate the effects of two different DNM2 mutations. First we identified a new alternatively spliced zebrafish dynamin-2a mRNA (dnm2a-v2) with greater similarity to human DNM2 than the deposited sequence. Then we knocked-down the zebrafish dnm2a, producing defects in muscle morphology. Finally, we expressed two mutated DNM2 mRNA by injecting zebrafish embryos with human mRNAs carrying the R522H mutation, causing CNM, or the G537C mutation, causing CMT. Defects arose especially in secondary motor neuron formation, with incorrect branching in embryos injected with CNM-mutated mRNA, and total absence of branching in those injected with CMT-mutated mRNA. Muscle morphology in embryos injected with CMT-mutated mRNA appeared less regularly organized than in those injected with CNM-mutated mRNA. Our results showing, a continuum between CNM and CMTDIB phenotypes in zebrafish, similarly to the human conditions, confirm this animal model to be a powerful tool to investigate mutations of DNM2 in vivo.
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Affiliation(s)
- Cinzia Bragato
- Neuromuscular Diseases and Neuroimmunology Unit, IRCCS Neurological Institute C. Besta, Milano, Italy
| | - Germano Gaudenzi
- Department of Biosciences, University of Milan, Via Celoria, 26, 20133, Milan, Italy
| | - Flavia Blasevich
- Neuromuscular Diseases and Neuroimmunology Unit, IRCCS Neurological Institute C. Besta, Milano, Italy
| | - Giulio Pavesi
- Department of Biosciences, University of Milan, Via Celoria, 26, 20133, Milan, Italy
| | - Lorenzo Maggi
- Neuromuscular Diseases and Neuroimmunology Unit, IRCCS Neurological Institute C. Besta, Milano, Italy
| | - Michele Giunta
- Neuromuscular Diseases and Neuroimmunology Unit, IRCCS Neurological Institute C. Besta, Milano, Italy
| | - Franco Cotelli
- Department of Biosciences, University of Milan, Via Celoria, 26, 20133, Milan, Italy
| | - Marina Mora
- Neuromuscular Diseases and Neuroimmunology Unit, IRCCS Neurological Institute C. Besta, Milano, Italy
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Fairgrieve MR, Shibata Y, Smith EK, Hayman ES, Luckenbach JA. Molecular characterization of the gonadal kisspeptin system: Cloning, tissue distribution, gene expression analysis and localization in sablefish (Anoplopoma fimbria). Gen Comp Endocrinol 2016; 225:212-223. [PMID: 26386183 DOI: 10.1016/j.ygcen.2015.07.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 07/02/2015] [Accepted: 07/21/2015] [Indexed: 10/23/2022]
Abstract
The kisspeptin system plays pivotal roles in the regulation of vertebrate reproduction. Classically, kisspeptin produced in the brain stimulates brain gonadotropin-releasing hormone signaling, which in turn activates the pituitary-gonad axis. Expression of the kisspeptin system has also been documented in peripheral tissues, including gonads of mammals and fishes. However, the fish gonadal kisspeptin system remained uncharacterized. Herein we report identification and characterization of four kisspeptin system mRNAs (kisspeptin 1 (kiss1), kiss2, and G protein-coupled receptor 54-1 (gpr54-1) and gpr54-2) in sablefish, Anoplopoma fimbria. Sablefish predicted protein sequences were highly similar to those of other marine teleosts, but less so to freshwater teleosts. Tissue distribution analyses revealed that all four kisspeptin-system transcripts were expressed in both brain and gonad. However, kiss2 was the predominant transcript in the gonads and the only transcript detected in ovulated eggs. Ontogenetic analysis of kiss2 expression in juvenile sablefish gonads demonstrated that levels were low during sex differentiation but increased with fish size and gonadal development. Dramatic increases in kiss2 mRNA occurred during primary oocyte growth, while levels remained relatively low in testes. In situ hybridization revealed that kiss2 mRNA was localized to cytoplasm of perinucleolus stage oocytes, suggesting it could play a local role in oogenesis or could be synthesized and stored within oocytes as maternal mRNA. This represents the first study to focus on the gonadal kisspeptin system in fishes and provides important tools for further investigation of both the gonadal and brain kisspeptin systems in sablefish.
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Affiliation(s)
- Marian R Fairgrieve
- Undergraduate Research Program, University of Washington, 171 Mary Gates Hall, Seattle, WA 98195-2803, USA
| | - Yasushi Shibata
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat St, Seattle, WA 98195-5020, USA
| | - Elizabeth K Smith
- Frank Orth and Associates, Under Contract to Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 2725 Montlake Blvd E, Seattle, WA 98112, USA
| | - Edward S Hayman
- Frank Orth and Associates, Under Contract to Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 2725 Montlake Blvd E, Seattle, WA 98112, USA
| | - J Adam Luckenbach
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, NOAA, 2725 Montlake Blvd E, Seattle, WA 98112, USA; Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA.
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Rozenfeld C, Butts IA, Tomkiewicz J, Zambonino-Infante JL, Mazurais D. Abundance of specific mRNA transcripts impacts hatching success in European eel, Anguilla anguilla L. Comp Biochem Physiol A Mol Integr Physiol 2016; 191:59-65. [DOI: 10.1016/j.cbpa.2015.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 08/19/2015] [Accepted: 09/18/2015] [Indexed: 11/28/2022]
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Dona M, Bachmann-Gagescu R, Texier Y, Toedt G, Hetterschijt L, Tonnaer EL, Peters TA, van Beersum SEC, Bergboer JGM, Horn N, de Vrieze E, Slijkerman RWN, van Reeuwijk J, Flik G, Keunen JE, Ueffing M, Gibson TJ, Roepman R, Boldt K, Kremer H, van Wijk E. NINL and DZANK1 Co-function in Vesicle Transport and Are Essential for Photoreceptor Development in Zebrafish. PLoS Genet 2015; 11:e1005574. [PMID: 26485514 PMCID: PMC4617706 DOI: 10.1371/journal.pgen.1005574] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 09/16/2015] [Indexed: 12/04/2022] Open
Abstract
Ciliopathies are Mendelian disorders caused by dysfunction of cilia, ubiquitous organelles involved in fluid propulsion (motile cilia) or signal transduction (primary cilia). Retinal dystrophy is a common phenotypic characteristic of ciliopathies since photoreceptor outer segments are specialized primary cilia. These ciliary structures heavily rely on intracellular minus-end directed transport of cargo, mediated at least in part by the cytoplasmic dynein 1 motor complex, for their formation, maintenance and function. Ninein-like protein (NINL) is known to associate with this motor complex and is an important interaction partner of the ciliopathy-associated proteins lebercilin, USH2A and CC2D2A. Here, we scrutinize the function of NINL with combined proteomic and zebrafish in vivo approaches. We identify Double Zinc Ribbon and Ankyrin Repeat domains 1 (DZANK1) as a novel interaction partner of NINL and show that loss of Ninl, Dzank1 or both synergistically leads to dysmorphic photoreceptor outer segments, accumulation of trans-Golgi-derived vesicles and mislocalization of Rhodopsin and Ush2a in zebrafish. In addition, retrograde melanosome transport is severely impaired in zebrafish lacking Ninl or Dzank1. We further demonstrate that NINL and DZANK1 are essential for intracellular dynein-based transport by associating with complementary subunits of the cytoplasmic dynein 1 motor complex, thus shedding light on the structure and stoichiometry of this important motor complex. Altogether, our results support a model in which the NINL-DZANK1 protein module is involved in the proper assembly and folding of the cytoplasmic dynein 1 motor complex in photoreceptor cells, a process essential for outer segment formation and function. The cytoplasmic dynein 1 motor complex is known to be essential for photoreceptor outer segment formation and function. NINL, an important interaction partner of three ciliopathy-associated proteins (lebercilin, USH2A and CC2D2A), was previously shown to associate with this motor complex. In this work, we scrutinize the role of NINL using a combination of affinity proteomics and zebrafish studies, in order to gain insight into the pathogenic mechanisms underlying these three associated hereditary disorders. We identify DZANK1 as an important interaction partner of NINL and show that loss of Ninl, Dzank1, or a combination of both synergistically results in impaired transport of trans Golgi-derived vesicles and, as a consequence, defective photoreceptor outer segment formation. Using affinity proteomics, we demonstrate that NINL and DZANK1 associate with complementary subunits of the cytoplasmic dynein 1 complex. Our results support a model in which the NINL-DZANK1 protein module is essential for the proper assembly and folding of the cytoplasmic dynein 1 motor complex, shedding light on the structure and stoichiometry of this important motor complex.
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Affiliation(s)
- Margo Dona
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Ruxandra Bachmann-Gagescu
- Institute of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
- Institute of Medical Genetics, University of Zurich, Zürich, Switzerland
| | - Yves Texier
- Division of Experimental Ophthalmology, and Medical Proteome Center, Centre for Ophthalmology, Eberhard Karls University Tuebingen, Tübingen, Germany
| | - Grischa Toedt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Lisette Hetterschijt
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Edith L. Tonnaer
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Theo A. Peters
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Sylvia E. C. van Beersum
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Judith G. M. Bergboer
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Nicola Horn
- Division of Experimental Ophthalmology, and Medical Proteome Center, Centre for Ophthalmology, Eberhard Karls University Tuebingen, Tübingen, Germany
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Ralph W. N. Slijkerman
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Jeroen van Reeuwijk
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Gert Flik
- Department of Organismal Animal Physiology, Institute for Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Jan E. Keunen
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Marius Ueffing
- Division of Experimental Ophthalmology, and Medical Proteome Center, Centre for Ophthalmology, Eberhard Karls University Tuebingen, Tübingen, Germany
| | - Toby J. Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ronald Roepman
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Karsten Boldt
- Division of Experimental Ophthalmology, and Medical Proteome Center, Centre for Ophthalmology, Eberhard Karls University Tuebingen, Tübingen, Germany
| | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
- * E-mail:
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Zhao HB, Zhang XY, Feng GQ, Guo MM, Chang P, Qi C, Zhong XP, Zhou QC, Wang JL. Expression of plzfa in embryo and adult of medaka Oryzias latipes. JOURNAL OF FISH BIOLOGY 2015; 87:231-240. [PMID: 26077174 DOI: 10.1111/jfb.12713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 04/22/2015] [Indexed: 06/04/2023]
Abstract
In this study, a homologous gene named plzfa was identified and characterized in medaka Oryzias latipes. Oryzias latipes plzfa was detected in all the tissues including brain, gill, muscle, liver, intestine, kidney, spleen, testis and ovary using reverse transcriptase (RT)-PCR. plzfa was detected in the oocytes of the ovary and in the spermatogonia and somitic cells of the testis by in situ hybridization. plzfa had a maternal origin with continuous and dynamic expression during embryonic development. plzfa was observed in the brain, neural rod and sensor organs including the eyes, ears and nose during embryogenesis. plzfa was also detected in the neural crest, somite, pectoral fin, intestine and skin. These results indicate that plzfa is a pleiotropic gene that may play major roles in various tissues.
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Affiliation(s)
- H B Zhao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - X Y Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - G Q Feng
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - M M Guo
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - P Chang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - C Qi
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - X P Zhong
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Q C Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - J L Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
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66
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Svoboda P, Franke V, Schultz RM. Sculpting the Transcriptome During the Oocyte-to-Embryo Transition in Mouse. Curr Top Dev Biol 2015; 113:305-49. [PMID: 26358877 DOI: 10.1016/bs.ctdb.2015.06.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In mouse, the oocyte-to-embryo transition entails converting a highly differentiated oocyte to totipotent blastomeres. This transition is driven by degradation of maternal mRNAs, which results in loss of oocyte identity, and reprogramming of gene expression during the course of zygotic gene activation, which occurs primarily during the two-cell stage and confers blastomere totipotency. Full-grown oocytes are transcriptionally quiescent and mRNAs are remarkably stable in oocytes due to the RNA-binding protein MSY2, which stabilizes mRNAs, and low activity of the 5' and 3' RNA degradation machinery. Oocyte maturation initiates a transition from mRNA stability to instability due to phosphorylation of MSY2, which makes mRNAs more susceptible to the RNA degradation machinery, and recruitment of dormant maternal mRNAs that encode for critical components of the 5' and 3' RNA degradation machinery. Small RNAs (miRNA, siRNA, and piRNA) play little, if any, role in mRNA degradation that occurs during maturation. Many mRNAs are totally degraded but a substantial fraction is only partially degraded, their degradation completed by the end of the two-cell stage. Genome activation initiates during the one-cell stage, is promiscuous, low level, and genome wide (and includes both inter- and intragenic regions) and produces transcripts that are inefficiently spliced and polyadenylated. The major wave of genome activation in two-cell embryos involves expression of thousands of new genes. This unique pattern of gene expression is the product of maternal mRNAs recruited during maturation that encode for transcription factors and chromatin remodelers, as well as dramatic changes in chromatin structure due to incorporation of histone variants and modified histones.
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Affiliation(s)
- Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
| | - Vedran Franke
- Bioinformatics Group, Division of Biology, Faculty of Science, Zagreb University, Zagreb, Croatia
| | - Richard M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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Molecular characterization and expression profile of three Fem-1 genes in Eriocheir sinensis provide a new insight into crab sex-determining mechanism. Comp Biochem Physiol B Biochem Mol Biol 2015; 189:6-14. [PMID: 26188322 DOI: 10.1016/j.cbpb.2015.07.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 06/25/2015] [Accepted: 07/07/2015] [Indexed: 02/02/2023]
Abstract
The FEM-1 protein of Caenorhabditis elegans plays a crucial role in the nematode sex-determination pathway. Here, we reported the characterization of three members of Fem-1 gene family in Eriocheir sinensis (designated EsFem-1a, EsFem-1b, and EsFem-1c), which were homologs of the nematode FEM-1 protein. The amino acid sequences of EsFem-1a, EsFem-1b, and EsFem-1c contained eight, nine, and eight ankyrin repeats, respectively. None of the ankyrin repeats had its own specific signature, and the evolution of ankyrin repeat was not completely independent. The predicted three-dimensional structure of EsFem-1 proteins exhibited highly similar superhelical conformation, especially the N-terminal six contiguous ankyrin repeats, which provided a binding surface for the protein-protein interaction. Phylogenetic tree based on the amino acid sequences revealed that EsFem-1a, EsFem-1b, and EsFem-1c were divided into three obvious separated clades. EsFem-1 genes were highly expressed in fertilized egg, 2-4 cell and blastula stage comparing with larval stage (P<0.01), which suggested they might be maternal genes. They also showed a certain degree of sexually dimorphic expression in some tissues. Notably, the highest expression of EsFem-1a was in the hepatopancreas, with EsFem-1b in testes and EsFem-1c in muscle (P<0.05), which indicated their potential role in a broad array of tissues. In addition, the genes initially involved in sex differentiation were not limited to those specifically expressed in the developing gonad. Taken together, these results suggested that EsFem-1 might function in crab early sex determination and late gonad development. The identification of Fem-1 gene family in E. sinensis provides a new insight into crab sex-determination mechanism.
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68
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Desvignes T, Nguyen T, Chesnel F, Bouleau A, Fauvel C, Bobe J. X-Linked Retinitis Pigmentosa 2 Is a Novel Maternal-Effect Gene Required for Left-Right Asymmetry in Zebrafish. Biol Reprod 2015; 93:42. [PMID: 26134862 DOI: 10.1095/biolreprod.115.130575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 06/10/2015] [Indexed: 01/05/2023] Open
Abstract
Retinitis pigmentosa 2 (RP2) gene is responsible for up to 20% of X-linked retinitis pigmentosa, a severe heterogeneous genetic disorder resulting in progressive retinal degeneration in humans. In vertebrates, several bodies of evidence have clearly established the role of Rp2 protein in cilia genesis and/or function. Unexpectedly, some observations in zebrafish have suggested the oocyte-predominant expression of the rp2 gene, a typical feature of maternal-effect genes. In the present study, we investigate the maternal inheritance of rp2 gene products in zebrafish eggs in order to address whether rp2 could be a novel maternal-effect gene required for normal development. Although both rp2 mRNA and corresponding protein are expressed during oogenesis, rp2 mRNA is maternally inherited, in contrast to Rp2 protein. A knockdown of the protein transcribed from both rp2 maternal and zygotic mRNA results in delayed epiboly and severe developmental defects, including eye malformations, that were not observed when only the protein from zygotic origin was knocked down. Moreover, the knockdown of maternal and zygotic Rp2 revealed a high incidence of left-right asymmetry establishment defects compared to only zygotic knockdown. Here we show that rp2 is a novel maternal-effect gene exclusively expressed in oocytes within the zebrafish ovary and demonstrate that maternal rp2 mRNA is essential for successful embryonic development and thus contributes to egg developmental competence. Our observations also reveal that Rp2 protein translated from maternal mRNA is important to allow normal heart loop formation, thus providing evidence of a direct maternal contribution to left-right asymmetry establishment.
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Affiliation(s)
- Thomas Desvignes
- INRA, UR1037 Fish Physiology and Genomics, Campus de Beaulieu, Rennes, France IFREMER, LALR, Palavas Les Flots, France
| | - Thaovi Nguyen
- INRA, UR1037 Fish Physiology and Genomics, Campus de Beaulieu, Rennes, France
| | | | - Aurélien Bouleau
- INRA, UR1037 Fish Physiology and Genomics, Campus de Beaulieu, Rennes, France IFREMER, LALR, Palavas Les Flots, France
| | | | - Julien Bobe
- INRA, UR1037 Fish Physiology and Genomics, Campus de Beaulieu, Rennes, France
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69
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Huang Y, Linsen SEV. Partial depletion of yolk during zebrafish embryogenesis changes the dynamics of methionine cycle and metabolic genes. BMC Genomics 2015; 16:427. [PMID: 26040990 PMCID: PMC4455928 DOI: 10.1186/s12864-015-1654-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 05/21/2015] [Indexed: 12/21/2022] Open
Abstract
Background Limited nutrient availability during development is associated with metabolic diseases in adulthood. The molecular cause for these defects is unclear. Here, we investigate if transcriptional changes caused by developmental malnutrition reveal an early response that can be linked to metabolism and metabolic diseases. Results We limited nutrient availability by removing yolk from zebrafish (Danio rerio) embryos. We then measured genome expression after 8, 24, 32 h post-fertilization (hpf) by RNA sequencing and 48 hpf by microarray profiling. We assessed the functional impact of deregulated genes by enrichment analysis of gene ontologies, pathways and CpG sites around the transcription start sites. Nutrient depletion during embryogenesis does not affect viability, but induces a bias towards female development. It induces subtle expression changes of metabolic genes: lipid transport, oxidative signaling, and glycolysis are affected during earlier stages, and hormonal signaling at 48 hpf. Co-citation analysis indicates association of deregulated genes to the metabolic syndrome, a known outcome of early-life nutrient depletion. Notably, deregulated methionine cycle genes indicate altered methyl donor availability. We find that the regulation of deregulated genes may be less dependent on methyl donor availability. Conclusions The systemic response to reduced nutrient availability in zebrafish embryos affects metabolic pathways and can be linked to metabolic diseases. Further exploration of the reported zebrafish model system may elucidate the consequences of reduced nutrient availability during embryogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1654-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunxian Huang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Sam E V Linsen
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
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Wang K, Nishida H. REGULATOR: a database of metazoan transcription factors and maternal factors for developmental studies. BMC Bioinformatics 2015; 16:114. [PMID: 25880930 PMCID: PMC4411712 DOI: 10.1186/s12859-015-0552-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/25/2015] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Genes encoding transcription factors that constitute gene-regulatory networks and maternal factors accumulating in egg cytoplasm are two classes of essential genes that play crucial roles in developmental processes. Transcription factors control the expression of their downstream target genes by interacting with cis-regulatory elements. Maternal factors initiate embryonic developmental programs by regulating the expression of zygotic genes and various other events during early embryogenesis. RESULTS This article documents the transcription factors of 77 metazoan species as well as human and mouse maternal factors. We improved the previous method using a statistical approach adding Gene Ontology information to Pfam based identification of transcription factors. This method detects previously un-discovered transcription factors. The novel features of this database are: (1) It includes both transcription factors and maternal factors, although the number of species, in which maternal factors are listed, is limited at the moment. (2) Ontological representation at the cell, tissue, organ, and system levels has been specially designed to facilitate development studies. This is the unique feature in our database and is not available in other transcription factor databases. CONCLUSIONS A user-friendly web interface, REGULATOR ( http://www.bioinformatics.org/regulator/ ), which can help researchers to efficiently identify, validate, and visualize the data analyzed in this study, are provided. Using this web interface, users can browse, search, and download detailed information on species of interest, genes, transcription factor families, or developmental ontology terms.
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Affiliation(s)
- Kai Wang
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan.
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Michalik O, Dobosz S, Zalewski T, Sapota M, Ocalewicz K. Induction of Gynogenetic and Androgenetic Haploid and Doubled Haploid Development in the Brown Trout (Salmo trutta
Linnaeus 1758). Reprod Domest Anim 2015; 50:256-262. [DOI: 10.1111/rda.12480] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/04/2014] [Indexed: 11/27/2022]
Affiliation(s)
- O Michalik
- Department of Molecular Evolution; University of Gdansk; Gdansk Poland
| | - S Dobosz
- Department of Salmonid Research; Inland Fisheries Institute in Olsztyn; Rutki Zukowo Poland
| | - T Zalewski
- Department of Salmonid Research; Inland Fisheries Institute in Olsztyn; Rutki Zukowo Poland
| | - M Sapota
- Department of Marine Biology and Ecology; Institute of Oceanography; University of Gdansk; Gdynia Poland
| | - K Ocalewicz
- Department of Marine Biology and Ecology; Institute of Oceanography; University of Gdansk; Gdynia Poland
- Department of Ichthyology; University of Warmia and Mazury in Olsztyn; Olsztyn Poland
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72
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Shaya L, Dejong C, Wilson JY. Expression patterns of cytochrome P450 3B and 3C genes in model fish species. Comp Biochem Physiol C Toxicol Pharmacol 2014; 166:115-25. [PMID: 25073111 DOI: 10.1016/j.cbpc.2014.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 06/12/2014] [Accepted: 06/15/2014] [Indexed: 11/28/2022]
Abstract
Cytochrome P450 (CYP) 3 enzymes are highly expressed in detoxification organs and play an important role in xenobiotic metabolism. In fish, the CYP3 family is diversified and includes several subfamilies (CYP3B, CYP3C, and CYP3D) not found in mammals. The functional role and expression patterns of these novel genes are unknown. In this study, the expression patterns of novel teleost CYP3 genes were determined in medaka(Oryzias latipes; CYP3B4, CYP3B5, CYP3B6) and zebrafish (Danio rerio; CYP3C1, CYP3C2, CYP3C3, CYP3C4), two important model fish species. Expression was quantified with real time PCR in multiple internal organs from adult male and female fish. CYP3C gene expression was determined in zebrafish embryos. Expression in all organs was detected for all genes, except for CYP3B4 in male organs. CYP3C1, CYP3C3, CYP3B4, CYP3B5, and CYP3B6 were more highly expressed in liver and/or intestine from at least one gender, suggesting a role in xenobiotic metabolism. Expression of CYP3C1 and CYP3B5 in olfactory rosette was comparable to liver. CYP3C1, CYP3C4, CYP3B5 and CYP3B6 expression was higher in the female organs; CYP3C2 and CYP3B5 were higher in testis. Estrogen and androgen response elements were found upstream of the start site of many of these genes raising the hypothesis that they are under steroid regulation. CYP3C1-3 were expressed in all developmental stages examined and appear to be maternally deposited. The expression patterns suggest that some of these CYP genes are involved in xenobiotic metabolism.
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Affiliation(s)
- Lana Shaya
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
| | - Chris Dejong
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
| | - Joanna Y Wilson
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada.
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Ge X, Grotjahn D, Welch E, Lyman-Gingerich J, Holguin C, Dimitrova E, Abrams EW, Gupta T, Marlow FL, Yabe T, Adler A, Mullins MC, Pelegri F. Hecate/Grip2a acts to reorganize the cytoskeleton in the symmetry-breaking event of embryonic axis induction. PLoS Genet 2014; 10:e1004422. [PMID: 24967891 PMCID: PMC4072529 DOI: 10.1371/journal.pgen.1004422] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 04/20/2014] [Indexed: 11/18/2022] Open
Abstract
Maternal homozygosity for three independent mutant hecate alleles results in embryos with reduced expression of dorsal organizer genes and defects in the formation of dorsoanterior structures. A positional cloning approach identified all hecate mutations as stop codons affecting the same gene, revealing that hecate encodes the Glutamate receptor interacting protein 2a (Grip2a), a protein containing multiple PDZ domains known to interact with membrane-associated factors including components of the Wnt signaling pathway. We find that grip2a mRNA is localized to the vegetal pole of the oocyte and early embryo, and that during egg activation this mRNA shifts to an off-center vegetal position corresponding to the previously proposed teleost cortical rotation. hecate mutants show defects in the alignment and bundling of microtubules at the vegetal cortex, which result in defects in the asymmetric movement of wnt8a mRNA as well as anchoring of the kinesin-associated cargo adaptor Syntabulin. We also find that, although short-range shifts in vegetal signals are affected in hecate mutant embryos, these mutants exhibit normal long-range, animally directed translocation of cortically injected dorsal beads that occurs in lateral regions of the yolk cortex. Furthermore, we show that such animally-directed movement along the lateral cortex is not restricted to a single arc corresponding to the prospective dorsal region, but occur in multiple meridional arcs even in opposite regions of the embryo. Together, our results reveal a role for Grip2a function in the reorganization and bundling of microtubules at the vegetal cortex to mediate a symmetry-breaking short-range shift corresponding to the teleost cortical rotation. The slight asymmetry achieved by this directed process is subsequently amplified by a general cortical animally-directed transport mechanism that is neither dependent on hecate function nor restricted to the prospective dorsal axis. One of the earliest and most crucial events in animal development is the establishment of the embryonic dorsal axis. In amphibians and fish, this event depends on the transport of so-called “dorsal determinants” from one region of the egg, at the pole opposite from the site where the oocyte nucleus lies, towards the site of axis induction. There, the dorsal determinant activates the Wnt signaling pathway, which in turn triggers dorsal gene expression. Dorsal determinant transport is mediated by the reorganization of a cellular network composed of microtubules. We determine that hecate, a zebrafish gene active during egg formation that is essential for embryonic axis induction, is required for an early step in this microtubule reorganization. We find that hecate corresponds to glutamate receptor interacting protein 2a, which participates in other animal systems in Wnt-based pathways. We also show that the microtubule reorganization dependent on hecate results in a subtle symmetry-breaking event that subsequently becomes amplified by a more general transport process independent of hecate function. Our data reveal new links between glutamate receptor interacting protein 2a, Wnt signaling and axis induction, and highlights basic mechanisms by which small changes early in development translate into global changes in the embryo.
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Affiliation(s)
- Xiaoyan Ge
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Danielle Grotjahn
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Elaine Welch
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Jamie Lyman-Gingerich
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Christiana Holguin
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Eva Dimitrova
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Elliot W. Abrams
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Tripti Gupta
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Florence L. Marlow
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Taijiro Yabe
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Anna Adler
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
| | - Mary C. Mullins
- Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Francisco Pelegri
- Laboratory of Genetics, University of Wisconsin – Madison, Madison, Wisconsin, United States of America
- * E-mail:
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Ovary transcriptome profiling via artificial intelligence reveals a transcriptomic fingerprint predicting egg quality in striped bass, Morone saxatilis. PLoS One 2014; 9:e96818. [PMID: 24820964 PMCID: PMC4018430 DOI: 10.1371/journal.pone.0096818] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/11/2014] [Indexed: 12/11/2022] Open
Abstract
Inherited gene transcripts deposited in oocytes direct early embryonic development in all vertebrates, but transcript profiles indicative of embryo developmental competence have not previously been identified. We employed artificial intelligence to model profiles of maternal ovary gene expression and their relationship to egg quality, evaluated as production of viable mid-blastula stage embryos, in the striped bass (Morone saxatilis), a farmed species with serious egg quality problems. In models developed using artificial neural networks (ANNs) and supervised machine learning, collective changes in the expression of a limited suite of genes (233) representing <2% of the queried ovary transcriptome explained >90% of the eventual variance in embryo survival. Egg quality related to minor changes in gene expression (<0.2-fold), with most individual transcripts making a small contribution (<1%) to the overall prediction of egg quality. These findings indicate that the predictive power of the transcriptome as regards egg quality resides not in levels of individual genes, but rather in the collective, coordinated expression of a suite of transcripts constituting a transcriptomic “fingerprint”. Correlation analyses of the corresponding candidate genes indicated that dysfunction of the ubiquitin-26S proteasome, COP9 signalosome, and subsequent control of the cell cycle engenders embryonic developmental incompetence. The affected gene networks are centrally involved in regulation of early development in all vertebrates, including humans. By assessing collective levels of the relevant ovarian transcripts via ANNs we were able, for the first time in any vertebrate, to accurately predict the subsequent embryo developmental potential of eggs from individual females. Our results show that the transcriptomic fingerprint evidencing developmental dysfunction is highly predictive of, and therefore likely to regulate, egg quality, a biologically complex trait crucial to reproductive fitness.
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75
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Lanes CFC, Bizuayehu TT, de Oliveira Fernandes JM, Kiron V, Babiak I. Transcriptome of Atlantic cod (Gadus morhua L.) early embryos from farmed and wild broodstocks. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:677-694. [PMID: 23887676 DOI: 10.1007/s10126-013-9527-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 05/24/2013] [Indexed: 06/02/2023]
Abstract
Significant efforts have been made to elucidate factors affecting egg quality in fish. Recently, we have shown that eggs originating from wild broodstock (WB) of Atlantic cod (Gadus morhua L.) are of superior quality to those derived from farmed broodstock (FB), and this is associated with differences in the chemical composition of egg yolk. However, maternal transcripts, accumulated during oogenesis, have not been studied extensively in fish. The aim of the present study was to characterize putative maternal mRNA transcriptome in fertilized eggs of Atlantic cod and to compare transcript pools between WB and FB in order to investigate the relation between egg developmental potential and putative maternal mRNA deposits. We performed high-throughput 454 pyrosequencing. For each WB and FB group, five cDNA libraries were individually tagged and sequenced, resulting in 98,687 (WB) and 119,333 (FB) average reads per library. Sequencing reads were de novo assembled, annotated, and mapped. Out of 13,726 identified isotigs, 238 were differentially expressed between WB and FB, with 155 isotigs significantly upregulated in WB. The sequence reads were mapped to 11,340 different Atlantic cod transcripts and 158 sequences were differentially expressed between the 2 groups. Important transcripts involved in fructose metabolism, fatty acid metabolism, glycerophospholipid metabolism, and oxidative phosphorylation were differentially represented between the two broodstock groups, showing potential as biomarkers of egg quality in teleosts. Our findings contribute to the hypothesis that maternal mRNAs affect egg quality and, consequently, the early development of fish.
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76
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Michalik O, Dobosz S, Wójcik I, Zalewski T, Ocalewicz K. Use of eggs derived from the interspecific charr hybrids to induce androgenetic development of the brook charr (Salvelinus fontinalis Mitchill 1814). Reprod Domest Anim 2013; 49:191-6. [PMID: 24219413 DOI: 10.1111/rda.12248] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 09/23/2013] [Indexed: 11/29/2022]
Abstract
Although, brook charr (Salvelinus fontinalis Mitchill 1814) and Arctic charr (Salvelinus alpinus Linnaeus 1758) are able to cross and give fertile offspring, their androgenetic nucleocytoplasmic hybrids are not viable. To overcome incompatibility between the egg cytoplasm of one charr species and the sperm nucleus of another charr species, application of F1 interspecific hybrids as egg donors for the purpose of androgenesis has been proposed. Here, androgenetic development of the brook charr was successfully induced in the brook charr eggs and the eggs derived from the reciprocal brook charr × Arctic charr F1 hybrids. A working androgenesis protocol included inactivation of the maternal nuclear DNA achieved by irradiation of the eggs with 420 Gy of X-rays, insemination of such treated eggs with the haploid sperm cells and exposition of the haploid androgenetic zygotes to the high hydrostatic pressure shock (51.711 MPa for 4 min) applied 420 min after insemination. Androgenetic larvae that hatched from the brook charr and the hybrid eggs were shown to be homozygous brook charr individuals. Androgenetic individuals exhibited 84 chromosomes and 100 chromosome arms (FN), values characteristic for the brook charr diploid cells. Strategy hybridize first than induce androgenesis should be tested in order to provide androgenetic offspring in other salmonids that are able to cross and produce fertile offspring.
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Affiliation(s)
- O Michalik
- Department of Molecular Evolution, University of Gdansk, Gdansk, Poland
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77
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Oliveira E, Casado M, Raldúa D, Soares A, Barata C, Piña B. Retinoic acid receptors' expression and function during zebrafish early development. J Steroid Biochem Mol Biol 2013; 138:143-51. [PMID: 23619336 DOI: 10.1016/j.jsbmb.2013.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 03/26/2013] [Accepted: 03/31/2013] [Indexed: 11/19/2022]
Abstract
Retinoic acid (RA) regulates many developmental processes through its binding to two types of nuclear receptors, the retinoic acid receptor (RAR), and the retinoid-X receptor (RXR), which preferentially binds to the 9-cis isomer. Here we analyzed the RAR/RXR regulatory system during the first 5 days of development of zebrafish. Analysis of the relative transcript abundances for the four RAR and the six RXR zebrafish genes present in the zebrafish genome indicates a transition from maternal to embryonic transcripts during the first 24h post fertilization. These changes did not affect the response to exogenous RA of the known RAR-responsive genes cyp26a1, dhrs3a, hoxb1b, hoxb5a, and hoxb5b. At the transcriptomic level, RA treatment elicited a negative feedback of genes involved in the endogenous RA synthesis and reduced levels of transcripts related to organ and anatomic development. These effects occurred at concentrations at which no morphological changes were observed. Data analysis suggests that exposure to exogenous RA results in an advance of the developing program, activating genes that should remain silent until later developmental stages and inhibiting expression of development-related genes. We conclude that zebrafish embryos are particularly sensitive to potential disruptors of the RAR/RXR regulatory system.
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Affiliation(s)
- Eva Oliveira
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona 18, 08034 Barcelona, Spain; CESAM & Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
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78
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Wei B, Guo Y, Zhai J, Su J, Han L, Kang C, Zhang Q. A study of the relationship between the Wnt/β-catenin signaling pathway and the gastrointestinal development of rat embryonic and perinatal periods. Exp Ther Med 2013; 5:1598-1602. [PMID: 23837038 PMCID: PMC3702624 DOI: 10.3892/etm.2013.1058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 03/08/2013] [Indexed: 11/28/2022] Open
Abstract
The Wnt/β-catenin signaling pathway plays a critical role in directing cell fate during the embryonic development of animals and humans. To investigate the effects of the Wnt/β-catenin signaling pathway on gastrointestinal development and differentiation, we studied the expression pattern of β-catenin, a key component of the pathway, in the gastrointestinal tissues of embryonic and perinatal rats. Immunohistochemistry was used to examine the expression levels of β-catenin in Sprague Dawley (SD) rat embryos at days 13, 18 and 21 and in SD rats at 1, 3, 7 and 28 days of age. We observed that the expression of β-catenin was greater and more diffuse in the gastrointestinal tissues of rat embryos at days 18 and 21 of gestation and in SD rats at days 1 and 3. In conclusion, our data suggest that β-catenin also plays an important role in the development of gastrointestinal tissues during the middle and late embryonic periods and the early postnatal period.
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Affiliation(s)
- Botao Wei
- Department of Gastroenterology, Tianjin Medical University General Hospital; Tianjin 300052, P.R. China ; Department of Infectious Disease, Tianjin Children's Hospital; Tianjin 300052, P.R. China
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79
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Fernández CG, Roufidou C, Antonopoulou E, Sarropoulou E. Expression of developmental-stage-specific genes in the gilthead sea bream Sparus aurata L. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2013; 15:313-320. [PMID: 23053055 DOI: 10.1007/s10126-012-9486-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 09/11/2012] [Indexed: 06/01/2023]
Abstract
The mechanism of early fish development as well as the control of egg quality is of great importance for the ability of the oocyte to develop after fertilization. Embryonic development is initially regulated by maternally provided mRNAs and later by the zygotic genome. Maternal mRNAs have an important role in initiating processes crucial to patterning the developing fish embryo. Furthermore, it has been shown that maternal RNA plays an important role in egg quality. The identification and characterization of candidate maternal genes in non-model fish species with important aquaculture interest like the gilthead sea bream Sparus aurata L. is of importance for future studies related to egg quality. The broodstock of the gilthead sea bream produces large quantities of eggs with a high and non-controllable quality variation. In the present study, we have studied the gene expression of 16 genes (gapdh 1 and 2, cathepsin D, L, S and Z, erk1, jnk1, p38 alpha and p38 delta, ppar alpha, beta and gamma, tubulin beta, ferritin M, cyclinA2) of different functional categories in seven developmental stages. The 16 genes were chosen based on their putative involvement in egg quality and regulation of early development. In total, 11 showed a characteristic gene expression pattern pinpointing to the possible function as maternal genes and thus may function as molecular biomarker for egg quality.
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Affiliation(s)
- Carmen García Fernández
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, P.O. Box 2214, 71003, Heraklion, Crete, Greece
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80
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Ocalewicz K, Kuzminski H, Pomianowski K, Dobosz S. Induction of androgenetic development of the brook charr (Salvelinus fontinalis)× Arctic charr (Salvelinus alpinus) hybrids in eggs derived from the parental species. Reprod Biol 2013; 13:105-12. [PMID: 23719114 DOI: 10.1016/j.repbio.2013.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 03/08/2013] [Accepted: 03/11/2013] [Indexed: 11/17/2022]
Abstract
Failure of interspecific androgenesis between brook charr (Salvelinus fontinalis, Mitchill 1814) and Arctic charr (Salvelinus alpinus, L.) has been attributed to the conflict between the egg cytoplasm of one species and the sperm nucleus of the other species. To overcome this incompatibility, sperm derived from the brook charr×Arctic charr hybrid male was used to induce androgenetic development in eggs originating from the parental species as well as their hybrids. The eggs were subjected to 420Gy of X-radiation to damage the maternal nuclear DNA and inseminated with untreated sperm. Haploid zygotes were exposed to high hydrostatic pressure shock (7000psi for 4min), which was applied 420min after insemination to inhibit the first cell cleavage and recover the diploid state of the zygote. The androgenetic diploid offspring that hatched from the brook charr, the Arctic charr and the hybrids eggs had survival rates of 4.7±0.6%, 1.2±0.4% and 16.8±0.5%, respectively. Drastic mortality among the hatched androgenetic individuals was observed within the first five months of rearing. Cytogenetic analysis of the androgenetic progenies exhibited residues of the irradiated maternal nuclear genome in the form of radiation-induced chromosome fragments in 47% of the specimens that were examined. Interactions between the egg cytoplasm and the sperm nucleus, the low quality of the gametes, the expression of homozygous paternal lethal alleles and the incomplete inactivation of the maternal chromosomes were identified as factors responsible for the large mortality among androgenetic embryos and hatchlings.
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Affiliation(s)
- Konrad Ocalewicz
- Department of Ichthyology, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 5, 10-719 Olsztyn, Poland.
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81
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Fernández J, Fuentes R. Fixation/permeabilization: new alternative procedure for immunofluorescence and mRNA in situ hybridization of vertebrate and invertebrate embryos. Dev Dyn 2013; 242:503-17. [PMID: 23389988 DOI: 10.1002/dvdy.23943] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2013] [Indexed: 11/10/2022] Open
Abstract
A new procedure is described to visualize the spatial pattern of expression of proteins and mRNAs in cryosections or whole-mounted leech, Drosophila, zebrafish, and chick embryos. Our principal contribution is in the use of a nonconventional fixation/permeabilization procedure based on the use of formaldehyde or paraformaldehyde combined with a short C-chain carboxylic acid. Detergents, methanol, and proteinases were omitted. Hybridization procedures were modified from those of routinely used protocols developed for the same embryos. Results showed that cytoskeletal and other cytoplasmic proteins, as well as different mRNAs, were clearly visualized in the expected regions of the embryos. Our procedure has several advantages over currently used protocols: is simpler, produces better general preservation of cells, yields reliable results, and can be used for embryos of different taxa at different developmental stages. It is hypothesized that short C-chain aliphatic carboxylic acids modulate the cross-linking effect of aldehyde fixatives on cell proteins.
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Affiliation(s)
- Juan Fernández
- Department of Biology, Faculty of Sciences, University of Chile, Santiago, Chile.
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82
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Okuthe GE. DNA and RNA pattern of staining during oogenesis in zebrafish (Danio rerio): a confocal microscopy study. Acta Histochem 2013; 115:178-84. [PMID: 22795267 DOI: 10.1016/j.acthis.2012.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 06/19/2012] [Accepted: 06/20/2012] [Indexed: 11/18/2022]
Abstract
Oogenesis involves a sequence of cellular divisions and developmental changes leading to the formation of oocytes, whose role in development is to transfer genomic information to the next generation. During this process, the gene expression pattern changes considerably concomitant with genome remodeling, while genomic information is maintained. The development of the gonad in zebrafish is unique in that it goes through an initial ovarian phase and subsequently into either ovarian or testicular phases. How the germ cells choose to commit to an oogenic fate and enter meiosis or alternatively not to enter meiosis and commit to a spermatogenetic fate remains a key question in development. Lack of suitable markers has hampered the understanding of the principles controlling sex differentiation in zebrafish. The current study was aimed at finding substantive cytochemical markers to identify specific oocyte stages primarily focusing on the DNA and RNA component of cells, using fluorescent dyes: acridine orange and propidium iodide. The pattern of synthesis and appearance of nucleoli was stage specific and may be used to identify stages of oogenesis. A distinguishing and possibly diagnostic feature of the staining pattern observed was the low level of chromatin staining compared to other cellular structures. This may be related to the more diffuse state of chromatin that occurs prior to thickening of chromosomes from the pachytene stage onwards. Although the fluorescent dyes may be useful in determining the localization of nucleic acids in tissue sections, it was not possible to quantify the relative contribution of the DNA and RNA components of specific stages of oocyte growth.
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Affiliation(s)
- Grace Emily Okuthe
- Department of Zoology, Walter Sisulu University, P/B X1 Mthatha, 5117, South Africa.
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83
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Gahr SA, Weber GM, Rexroad CE. Identification and expression of Smads associated with TGF-β/activin/nodal signaling pathways in the rainbow trout (Oncorhynchus mykiss). FISH PHYSIOLOGY AND BIOCHEMISTRY 2012; 38:1233-1244. [PMID: 22290475 DOI: 10.1007/s10695-012-9611-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 01/19/2012] [Indexed: 05/31/2023]
Abstract
The Smad proteins are essential components of the TGF-β/activin/nodal family signaling pathway. We report the identification and expression of transcripts representing three receptor Smads (Smad2a, Smad2b, and Smad3), two common Smads (Smad4a and Smad4b), and one inhibitory Smad (Smad7). Phylogenetic analysis suggests this gene family evolved through the combination of ancient and more recent salmonid genome duplication events. Tissue distribution, embryonic expression, and expression in growth hormone (GH) treated fish were assessed by reverse transcription PCR or qPCR. All six Smad transcripts were ubiquitously expressed in adult tissues. We observed the highest expression of the receptor Smads in unfertilized eggs, generally decreasing during early embryonic development and slightly increasing around 11 days post-fertilization (dpf). Smad7 expression was low for most of embryonic development, with a dramatic increase at the onset of muscle development (6 dpf), and at hatch (24 dpf). Smad4 expression was low during early embryonic development and increased after 14 dpf. The increased expression of Smad4 and Smad7 during late embryonic development may indicate modulation of gene expression by GH axis, which initiates activity during late embryonic development. These data were supported by the modulation of these Smads in the gill filament, stomach, and muscle following a GH treatment. Additionally, these changes are concurrent with the modulation of expression of TGF-β family members. Most significantly, the increased expression of Smad7 in the muscle is simultaneous with increased expression of MSTN1A and not MSTN1B during both embryonic development and following GH treatment. These data indicate a promyogenic role for Smad7 as previously identified in other non-fish species.
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Affiliation(s)
- Scott A Gahr
- Biology Department, St. Vincent College, 300 Fraser Purchase Rd., Latrobe, PA 15650, USA.
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84
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Lanes C, Fernandes J, Kiron V, Babiak I. Profiling of key apoptotic, stress, and immune-related transcripts during embryonic and postembryonic development of Atlantic cod (Gadus morhua L.). Theriogenology 2012; 78:1583-1596.e2. [DOI: 10.1016/j.theriogenology.2012.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 07/05/2012] [Accepted: 07/05/2012] [Indexed: 12/13/2022]
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85
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Stengel R, Rivera-Milla E, Sahoo N, Ebert C, Bollig F, Heinemann SH, Schönherr R, Englert C. Kcnh1 voltage-gated potassium channels are essential for early zebrafish development. J Biol Chem 2012; 287:35565-35575. [PMID: 22927438 PMCID: PMC3471731 DOI: 10.1074/jbc.m112.363978] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Kcnh1 gene encodes a voltage-gated potassium channel highly expressed in neurons and involved in tumor cell proliferation, yet its physiological roles remain unclear. We have used the zebrafish as a model to analyze Kcnh1 function in vitro and in vivo. We found that the kcnh1 gene is duplicated in teleost fish (i.e. kcnh1a and kcnh1b) and that both genes are maternally expressed during early development. In adult zebrafish, kcnh1a and kcnh1b have distinct expression patterns but share expression in brain and testis. Heterologous expression of both genes in Xenopus oocytes revealed a strong conservation of characteristic functional properties between human and fish channels, including a unique sensitivity to intracellular Ca2+/calmodulin and modulation of voltage-dependent gating by extracellular Mg2+. Using a morpholino antisense approach, we demonstrate a strong kcnh1 loss-of-function phenotype in developing zebrafish, characterized by growth retardation, delayed hindbrain formation, and embryonic lethality. This late phenotype was preceded by transcriptional up-regulation of known cell-cycle inhibitors (p21, p27, cdh2) and down-regulation of pro-proliferative factors, including cyclin D1, at 70% epiboly. These results reveal an unanticipated basic activity of kcnh1 that is crucial for early embryonic development and patterning.
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Affiliation(s)
- Rayk Stengel
- Friedrich Schiller University of Jena and Jena University Hospital, Center for Molecular Biomedicine, Department of Biophysics
| | - Eric Rivera-Milla
- Leibniz Institute for Age Research-Fritz Lipmann Institute, D-07745 Jena, Germany
| | - Nirakar Sahoo
- Friedrich Schiller University of Jena and Jena University Hospital, Center for Molecular Biomedicine, Department of Biophysics
| | - Christina Ebert
- Leibniz Institute for Age Research-Fritz Lipmann Institute, D-07745 Jena, Germany
| | - Frank Bollig
- Leibniz Institute for Age Research-Fritz Lipmann Institute, D-07745 Jena, Germany
| | - Stefan H Heinemann
- Friedrich Schiller University of Jena and Jena University Hospital, Center for Molecular Biomedicine, Department of Biophysics
| | - Roland Schönherr
- Friedrich Schiller University of Jena and Jena University Hospital, Center for Molecular Biomedicine, Department of Biophysics.
| | - Christoph Englert
- Leibniz Institute for Age Research-Fritz Lipmann Institute, D-07745 Jena, Germany
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86
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Amaral IPG, Johnston IA. Experimental selection for body size at age modifies early life-history traits and muscle gene expression in adult zebrafish. ACTA ACUST UNITED AC 2012; 215:3895-904. [PMID: 22899520 DOI: 10.1242/jeb.068908] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The short generation time of the zebrafish (Danio rerio) was exploited to investigate the effects of selection for body size at age on early life-history traits and on the transcriptional response to a growth stimulus in skeletal muscle of adult fish. Replicate populations were either unselected (U-lineage) or subjected to four generations of experimental selection for small (S-lineage) or large (L-lineage) body size at 90 days post-fertilization. Body mass was on average 16.3% and 41.0% higher in the L- than in the U- and S-lineages, respectively. Egg diameter was 6.4% lower with 13% less yolk in the S-lineage compared with the other lineages. Maternal transcripts for igf2r, bmpr1aa, igf1ar, igf2a, igfbp5a, ghra and igfbp3 in 2-4 cell stage embryos were higher in the L- than in the S-lineage. Larvae from the L-lineage were significantly larger, but survivorship at the end of the first month was similar between lineages. Gene expression was measured in the fast muscle of adult fish fasted for 7 days and then re-fed to satiation for 48 h. The expression of 11 insulin-like growth factor pathway genes and 12 other nutritionally responsive genes was similar for the S- and L-lineages as was gut fullness with feeding. Transcript abundance for four genes (igf1a, igf2r, igfbp1a and igfbp1b) showed either regulated or constitutive differences between the S- and L-lineages. For example, igf2 receptor transcript abundance was higher and igbp1a/b transcript abundance was lower in the L- than in the S-lineage, consistent with an effect of selection on insulin-like growth factor signalling.
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Affiliation(s)
- Ian P G Amaral
- Scottish Oceans Institute, School of Biology, University of St Andrews, St Andrews, Fife KY16 8LB, UK.
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87
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Lim S, Kumari P, Gilligan P, Quach HNB, Mathavan S, Sampath K. Dorsal activity of maternal squint is mediated by a non-coding function of the RNA. Development 2012; 139:2903-15. [PMID: 22721777 DOI: 10.1242/dev.077081] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite extensive study, the earliest steps of vertebrate axis formation are only beginning to be elucidated. We previously showed that asymmetric localization of maternal transcripts of the conserved zebrafish TGFβ factor Squint (Sqt) in 4-cell stage embryos predicts dorsal, preceding nuclear accumulation of β-catenin. Cell ablations and antisense oligonucleotides that deplete Sqt lead to dorsal deficiencies, suggesting that localized maternal sqt functions in dorsal specification. However, based upon analysis of sqt and Nodal signaling mutants, the function and mechanism of maternal sqt was debated. Here, we show that sqt RNA may function independently of Sqt protein in dorsal specification. sqt insertion mutants express localized maternal sqt RNA. Overexpression of mutant/non-coding sqt RNA and, particularly, the sqt 3'UTR, leads to ectopic nuclear β-catenin accumulation and expands dorsal gene expression. Dorsal activity of sqt RNA requires Wnt/β-catenin but not Oep-dependent Nodal signaling. Unexpectedly, sqt ATG morpholinos block both sqt RNA localization and translation and abolish nuclear β-catenin, providing a mechanism for the loss of dorsal identity in sqt morphants and placing maternal sqt RNA upstream of β-catenin. The loss of early dorsal gene expression can be rescued by the sqt 3'UTR. Our findings identify new non-coding functions for the Nodal genes and support a model wherein sqt RNA acts as a scaffold to bind and deliver/sequester maternal factors to future embryonic dorsal.
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Affiliation(s)
- Shimin Lim
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
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88
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Drivenes Ø, Taranger GL, Edvardsen RB. Gene expression profiling of Atlantic cod (Gadus morhua) embryogenesis using microarray. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2012; 14:167-176. [PMID: 21833508 DOI: 10.1007/s10126-011-9399-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Accepted: 06/26/2011] [Indexed: 05/31/2023]
Abstract
Atlantic cod (Gadus morhua) is a fish species of high importance, as a key species in a range of Northern ecosystems, in fisheries, and as an emerging species in aquaculture. So far, little is known about the transcriptional activity during early developmental stages of Atlantic cod. Hence, we decided to use a cDNA microarray covering 7,000 genes to analyze the temporal activity of the transcriptome during cod embryogenesis. Twelve different embryonic time points were selected, covering major developmental stages and processes such as maternally derived mRNA, blastula, gastrula, segmentation, hatching, and first-feeding larval stage. The microarray analysis revealed a highly dynamic transcriptional profile, showing for the first time the differential expression of thousands of known and unknown genes during Atlantic cod embryogenesis. These initial findings will serve as an important baseline for future in-depth studies of candidate genes involved in development, reproductive control, disease resistance, growth, nutrient digestion, and metabolism.
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Affiliation(s)
- Øyvind Drivenes
- Institute of Marine Research, P.O. Box 1870, Nordnes, 5817 Bergen, Norway
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89
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Salinas-Saavedra M, Vargas AO. Cortical cytasters: a highly conserved developmental trait of Bilateria with similarities to Ctenophora. EvoDevo 2011; 2:23. [PMID: 22133482 PMCID: PMC3248832 DOI: 10.1186/2041-9139-2-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 12/01/2011] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Cytasters (cytoplasmic asters) are centriole-based nucleation centers of microtubule polymerization that are observable in large numbers in the cortical cytoplasm of the egg and zygote of bilaterian organisms. In both protostome and deuterostome taxa, cytasters have been described to develop during oogenesis from vesicles of nuclear membrane that move to the cortical cytoplasm. They become associated with several cytoplasmic components, and participate in the reorganization of cortical cytoplasm after fertilization, patterning the antero-posterior and dorso-ventral body axes. PRESENTATION OF THE HYPOTHESIS The specific resemblances in the development of cytasters in both protostome and deuterostome taxa suggest that an independent evolutionary origin is unlikely. An assessment of published data confirms that cytasters are present in several protostome and deuterostome phyla, but are absent in the non-bilaterian phyla Cnidaria and Ctenophora. We hypothesize that cytasters evolved in the lineage leading to Bilateria and were already present in the most recent common ancestor shared by protostomes and deuterostomes. Thus, cytasters would be an ancient and highly conserved trait that is homologous across the different bilaterian phyla. The alternative possibility is homoplasy, that is cytasters have evolved independently in different lineages of Bilateria. TESTING THE HYPOTHESIS So far, available published information shows that appropriate observations have been made in eight different bilaterian phyla. All of them present cytasters. This is consistent with the hypothesis of homology and conservation. However, there are several important groups for which there are no currently available data. The hypothesis of homology predicts that cytasters should be present in these groups. Increasing the taxonomic sample using modern techniques uniformly will test for evolutionary patterns supporting homology, homoplasy, or secondary loss of cytasters. IMPLICATIONS OF THE HYPOTHESIS If cytasters are homologous and highly conserved across bilateria, their potential developmental and evolutionary relevance has been underestimated. The deep evolutionary origin of cytasters also becomes a legitimate topic of research. In Ctenophora, polyspermic fertilization occurs, with numerous sperm entering the egg. The centrosomes of sperm pronuclei associate with cytoplasmic components of the egg and reorganize the cortical cytoplasm, defining the oral-aboral axis. These resemblances lead us to suggest the possibility of a polyspermic ancestor in the lineage leading to Bilateria.
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Affiliation(s)
- Miguel Salinas-Saavedra
- Laboratory of Ontogeny and Phylogeny, Department of Biology, Faculty of Science, University of Chile. Las Palmeras, Ñuñoa, Casilla 653, Santiago, Chile
| | - Alexander O Vargas
- Laboratory of Ontogeny and Phylogeny, Department of Biology, Faculty of Science, University of Chile. Las Palmeras, Ñuñoa, Casilla 653, Santiago, Chile
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90
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Sapetto-Rebow B, McLoughlin SC, O'Shea LC, O'Leary O, Willer JR, Alvarez Y, Collery R, O'Sullivan J, Van Eeden F, Hensey C, Kennedy BN. Maternal topoisomerase II alpha, not topoisomerase II beta, enables embryonic development of zebrafish top2a-/- mutants. BMC DEVELOPMENTAL BIOLOGY 2011; 11:71. [PMID: 22111588 PMCID: PMC3287258 DOI: 10.1186/1471-213x-11-71] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 11/23/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND Genetic alterations in human topoisomerase II alpha (TOP2A) are linked to cancer susceptibility. TOP2A decatenates chromosomes and thus is necessary for multiple aspects of cell division including DNA replication, chromosome condensation and segregation. Topoisomerase II alpha is also required for embryonic development in mammals, as mouse Top2a knockouts result in embryonic lethality as early as the 4-8 cell stage. The purpose of this study was to determine whether the extended developmental capability of zebrafish top2a mutants arises from maternal expression of top2a or compensation from its top2b paralogue. RESULTS Here, we describe bloody minded (blm), a novel mutant of zebrafish top2a. In contrast to mouse Top2a nulls, zebrafish top2a mutants survive to larval stages (4-5 day post fertilization). Developmental analyses demonstrate abundant expression of maternal top2a but not top2b. Inhibition or poisoning of maternal topoisomerase II delays embryonic development by extending the cell cycle M-phase. Zygotic top2a and top2b are co-expressed in the zebrafish CNS, but endogenous or ectopic top2b RNA appear unable to prevent the blm phenotype. CONCLUSIONS We conclude that maternal top2a enables zebrafish development before the mid-zygotic transition (MZT) and that zebrafish top2a and top2b are not functionally redundant during development after activation of the zygotic genome.
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Affiliation(s)
- Beata Sapetto-Rebow
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
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91
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Groh KJ, Nesatyy VJ, Segner H, Eggen RIL, Suter MJF. Global proteomics analysis of testis and ovary in adult zebrafish (Danio rerio). FISH PHYSIOLOGY AND BIOCHEMISTRY 2011; 37:619-647. [PMID: 21229308 PMCID: PMC3146978 DOI: 10.1007/s10695-010-9464-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Accepted: 12/17/2010] [Indexed: 05/27/2023]
Abstract
The molecular mechanisms controlling sex determination and differentiation in zebrafish (Danio rerio) are largely unknown. A genome-wide analysis may provide comprehensive insights into the processes involved. The mRNA expression in zebrafish gonads has been fairly well studied, but much less data on the corresponding protein expression are available, although the proteins are considered to be more relevant markers of gene function. Because mRNA and protein abundances rarely correlate well, mRNA profiles need to be complemented with the information on protein expression. The work presented here analyzed the proteomes of adult zebrafish gonads by a multidimensional protein identification technology, generating the to-date most populated lists of proteins expressed in mature zebrafish gonads. The acquired proteomics data partially confirmed existing transcriptomics information for several genes, including several novel transcripts. However, disagreements between mRNA and protein abundances were often observed, further stressing the necessity to assess the expression on different levels before drawing conclusions on a certain gene's expression and function. Several gene groups expressed in a sexually dimorphic way in zebrafish gonads were identified. Their potential importance for gonad development and function is discussed. The data gained in the current study provide a basis for further work on elucidating processes occurring during zebrafish development with use of high-throughput proteomics.
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Affiliation(s)
- Ksenia J. Groh
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Environmental Toxicology, Überlandstrasse 133, Postbox 611, 8600 Dübendorf, Switzerland
| | - Victor J. Nesatyy
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Environmental Toxicology, Überlandstrasse 133, Postbox 611, 8600 Dübendorf, Switzerland
- Present Address: EPFL, Station 15, 1015 Lausanne, Switzerland
| | - Helmut Segner
- Centre for Fish and Wildlife Health, University of Bern, Länggassstrasse 122, Postbox 8466, 3001 Bern, Switzerland
| | - Rik I. L. Eggen
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Environmental Toxicology, Überlandstrasse 133, Postbox 611, 8600 Dübendorf, Switzerland
| | - Marc J.-F. Suter
- Eawag: Swiss Federal Institute of Aquatic Science and Technology, Environmental Toxicology, Überlandstrasse 133, Postbox 611, 8600 Dübendorf, Switzerland
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92
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Zhang JE, Luo A, Xin HP, Zhao J, Li SS, Qu LH, Ma LG, Scholten S, Sun MX. Genes of both parental origins are differentially involved in early embryogenesis of a tobacco interspecies hybrid. PLoS One 2011; 6:e23153. [PMID: 21829711 PMCID: PMC3150392 DOI: 10.1371/journal.pone.0023153] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 07/12/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In animals, early embryonic development is largely dependent on maternal transcripts synthesized during gametogenesis. However, in higher plants, the extent of maternal control over zygote development and early embryogenesis is not fully understood yet. Nothing is known about the activity of the parental genomes during seed formation of interspecies hybrids. METHODOLOGY/PRINCIPAL FINDINGS Here, we report that an interspecies hybridization system between SR1 (Nicotiana tabacum) and Hamayan (N. rustica) has been successfully established. Based on the system we selected 58 genes that have polymorphic sites between SR1 and Hamayan, and analyzed the allele-specific expression of 28 genes in their hybrid zygotes (Hamayan x SR1). Finally the allele-specific expressions of 8 genes in hybrid zygotes were repeatedly confirmed. Among them, 4 genes were of paternal origin, 1 gene was of maternal origin and 3 genes were of biparental origin. These results revealed obvious biparental involvement and differentially contribution of parental-origin genes to zygote development in the interspecies hybrid. We further detected the expression pattern of the genes at 8-celled embryo stage found that the involvement of the parental-origin genes may change at different stages of embryogenesis. CONCLUSIONS/SIGNIFICANCE We reveal that genes of both parental origins are differentially involved in early embryogenesis of a tobacco interspecies hybrid and functions in a developmental stage-dependent manner. This finding may open a window to seek for the possible molecular mechanism of hybrid vigor.
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Affiliation(s)
- Jun-E Zhang
- Key Laboratory of Ministry of Education for Plant Development Biology, College of Life Science, Wuhan University, Wuhan, China
- College of Life Science, Jiangxi Normal University, Nanchang, China
| | - An Luo
- Key Laboratory of Ministry of Education for Plant Development Biology, College of Life Science, Wuhan University, Wuhan, China
| | - Hai-Ping Xin
- Key Laboratory of Ministry of Education for Plant Development Biology, College of Life Science, Wuhan University, Wuhan, China
| | - Jing Zhao
- Key Laboratory of Ministry of Education for Plant Development Biology, College of Life Science, Wuhan University, Wuhan, China
| | - Shi-Sheng Li
- Key Laboratory of Ministry of Education for Plant Development Biology, College of Life Science, Wuhan University, Wuhan, China
| | - Liang-Huan Qu
- Key Laboratory of Ministry of Education for Plant Development Biology, College of Life Science, Wuhan University, Wuhan, China
| | - Li-Gang Ma
- Key Laboratory of Ministry of Education for Plant Development Biology, College of Life Science, Wuhan University, Wuhan, China
| | - Stefan Scholten
- Biocenter Klein Flottbek, Developmental Biology and Biotechnology, University of Hamburg, Hamburg, Germany
| | - Meng-Xiang Sun
- Key Laboratory of Ministry of Education for Plant Development Biology, College of Life Science, Wuhan University, Wuhan, China
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93
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Celeghin A, Benato F, Pikulkaew S, Rabbane MG, Colombo L, Dalla Valle L. The knockdown of the maternal estrogen receptor 2a (esr2a) mRNA affects embryo transcript contents and larval development in zebrafish. Gen Comp Endocrinol 2011; 172:120-9. [PMID: 21199655 DOI: 10.1016/j.ygcen.2010.12.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 12/21/2010] [Accepted: 12/22/2010] [Indexed: 10/18/2022]
Abstract
In zebrafish, ovulated oocytes are loaded with maternal estrogen receptor 2a (esr2a) mRNA which is spread as granular and filamentous structures throughout the central ooplasm and is promptly relocated inside the blastodisc area at the 1-cell stage (0.2h post-fertilization, hpf), as shown by in situ hybridization. This transcript is available for translation until its sharp decline from 4 to 8 hpf, being replaced by low levels of zygotic esr2a mRNA mainly localized in the head region and around the yolk sac from 24 hpf until hatching at 48 hpf. To test the functional role of the maternal esr2a mRNA, 1- or 2-cell embryos were injected with 10.3 ng each of morpholino (MO) to knockdown translation (MO2-esr2a) of both maternal and zygotic esr2a transcripts, with a missplicing MO (MO3-esr2a) to effectively block post-transcriptionally the zygotic transcript alone, and with a non-specific MO-control. Treatment with MO2-esr2a increased apoptosis in embryos, especially in the brain, and caused severe malformations in 63% of 1-5 dpf larvae, as compared to 10-11% in those treated with MO3-esr2a and MO-control. Defects included body growth delay with curved shape, persistent yolk sac with reduced sub-intestinal veins and swollen yolk extension, abnormal brain and splanchnocranium development, smaller eyes and otic vesicles, pericardial oedema, uninflated swim bladder and rudimentary caudal fin with aberrant circular swimming. Affected larvae could survive for only 12-14 days. The MO2-esr2a phenotype was rescued with co-injection of 30 pg/embryo of mutated zebrafish esr2a mRNA encoding the full length of Esr2a, but containing eight silent mutations in the region recognised by MO2-esr2a. A lower dosage (15 pg) failed to recover mortality and abnormality. Raising the dosage to 60 and 90 pg increased abnormality, but not mortality, whereas with 120 pg both mortality and abnormality worsened, indicating a strict quantitative requirement of Esr2a. Co-injection of an anti-p53 MO failed to rescue the MO2-esr2a phenotype, eliminating the possibility of off-target effects. Pangenomic microarray analysis revealed that 240 and 219 significantly expressed transcripts were up- and down-regulated, respectively, by maternal Esr2a protein deficiency in 8-hpf MO2-esr2a embryos. Also at 48 hpf, 162 and 120 presumably zygotic transcripts were up- and down-regulated, respectively, but only 18 were in common with each of the 8-hpf sets. In total, the transcripts from 705 genes were affected by Esr2a knockdown. These findings suggest the involvement of maternal esr2a mRNA, presumably transactivated by maternal 17β-estradiol stored in the oocyte from enveloping granulosa cells, in the epigenetic programming of zebrafish development.
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MESH Headings
- Animals
- Animals, Genetically Modified
- Cartilage/embryology
- Cartilage/growth & development
- Cartilage/metabolism
- Embryo, Nonmammalian/chemistry
- Embryo, Nonmammalian/metabolism
- Epigenesis, Genetic/physiology
- Estrogen Receptor beta
- Gene Expression Profiling
- Gene Expression Regulation, Developmental
- Gene Knockdown Techniques
- Larva/genetics
- Larva/growth & development
- Larva/metabolism
- Microarray Analysis
- Phenotype
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Messenger, Stored/antagonists & inhibitors
- RNA, Messenger, Stored/genetics
- Receptors, Estrogen/antagonists & inhibitors
- Receptors, Estrogen/genetics
- Receptors, Estrogen/metabolism
- Validation Studies as Topic
- Zebrafish/embryology
- Zebrafish/genetics
- Zebrafish/growth & development
- Zebrafish/metabolism
- Zebrafish Proteins/antagonists & inhibitors
- Zebrafish Proteins/genetics
- Zebrafish Proteins/metabolism
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Affiliation(s)
- Andrea Celeghin
- Comparative Endocrinology Laboratory, Department of Biology, University of Padova, Via U. Bassi 58/B, 35131 Padova, Italy
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94
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Matsuda Y, Ito Y, Hashimoto H, Yokoi H, Suzuki T. Detection of vitellogenin incorporation into zebrafish oocytes by FITC fluorescence. Reprod Biol Endocrinol 2011; 9:45. [PMID: 21481233 PMCID: PMC3080286 DOI: 10.1186/1477-7827-9-45] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Accepted: 04/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Large volumes of lymph can be collected from the eye-sacs of bubble-eye goldfish. We attempted to induce vitellogenin (Vtg) in the eye-sac lymph of bubble-eye goldfish and develop a method for visualizing Vtg incorporation by zebrafish oocytes using FITC-labeling. METHODS Estrogen efficiently induced Vtg in the eye-sac lymph of goldfish. After FITC-labeled Vtg was prepared, it was injected into mature female zebrafish. RESULTS Incorporation of FITC-labeled Vtg by zebrafish oocytes was detected in in vivo and in vitro experiments. The embryos obtained from zebrafish females injected with FITC-labeled Vtg emitted FITC fluorescence from the yolk sac and developed normally. CONCLUSION This method for achieving Vtg incorporation by zebrafish oocytes could be useful in experiments related to the development and endocrinology of zebrafish oocytes.
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Affiliation(s)
- Yohei Matsuda
- Laboratory of Marine Life Science and Genetics, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 981-8555, Japan
| | - Yoshie Ito
- Laboratory of Marine Life Science and Genetics, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 981-8555, Japan
- Industrial Technology Institute, Miyagi Prefectural Government, Sendai, 981-3206, Japan
| | - Hisashi Hashimoto
- Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601, Japan
| | - Hayato Yokoi
- Laboratory of Marine Life Science and Genetics, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 981-8555, Japan
| | - Tohru Suzuki
- Laboratory of Marine Life Science and Genetics, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 981-8555, Japan
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95
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Martinelli M, Carinci F, Morselli P, Caramelli E, Palmieri A, Girardi A, Riberti C, Scapoli L. Evidence of LEF1 Fetal-Maternal Interaction in Cleft Lip with or without Cleft Palate in a Consistent Italian Sample Study. Int J Immunopathol Pharmacol 2011; 24:15-9. [DOI: 10.1177/03946320110240s204] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Epithelial mesenchymal transformation is considered a cardinal process in orofacial development. Several molecular players appear to be involved in this delicate mechanism; the activation of LEF1 transcription factor by transforming growth factor beta 3 seems to be a key step for the correct flow of events. The failure of orofacial processes during embryonic development may provoke cleft lip and/or cleft palate malformations. The scope of the present investigation was to verify whether genetic variants at LEF1 could influence the risk of orofacial clefting. The approach was a family based association study involving a total of 512 Italian patients and their parents, 401 having cleft lip with or without cleft palate (CL/P) and 111 with cleft palate only (CPO). Haplotype association analysis provided moderate evidence of an association with clefting (p 0.01). A log-linear likelihood-based method was used to verify maternal and foetal-maternal association. An association between the maternal genotype and the occurrence of CL/P was observed at two polymorphic loci, at rs10022956 (P = 0.0049) and rs10025431 (P = 0.0065) respectively, while a foetal-maternal effect modulating the risk of clefting was found at locus rs10025431 (P = 0.0071). These data further corroborate the importance of the mother's genotype with regard to susceptibility to malformations and early-onset diseases.
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Affiliation(s)
- M. Martinelli
- Department of Histology, Embryology and Applied Biology, Centre of Molecular Genetics, CARISBO Foundation, University of Bologna, Bologna, Italy
| | - F. Carinci
- Department of D.M.C.C.C., Section of Maxillofacial and Plastic Surgery, University of Ferrara, Ferrara, Italy
| | - P.G. Morselli
- University of Bologna - School of Plastic Surgery - Plastic Surgery Unit S. Orsola Hospital, Bologna, Italy
| | - E. Caramelli
- Department of Histology, Embryology and Applied Biology, Centre of Molecular Genetics, CARISBO Foundation, University of Bologna, Bologna, Italy
| | - A. Palmieri
- Department of D.M.C.C.C., Section of Maxillofacial and Plastic Surgery, University of Ferrara, Ferrara, Italy
| | - A. Girardi
- Department of Histology, Embryology and Applied Biology, Centre of Molecular Genetics, CARISBO Foundation, University of Bologna, Bologna, Italy
| | - C. Riberti
- Department of D.M.C.C.C., Section of Maxillofacial and Plastic Surgery, University of Ferrara, Ferrara, Italy
| | - L. Scapoli
- Department of Histology, Embryology and Applied Biology, Centre of Molecular Genetics, CARISBO Foundation, University of Bologna, Bologna, Italy
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96
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Desvignes T, Fauvel C, Bobe J. The NME gene family in zebrafish oogenesis and early development. Naunyn Schmiedebergs Arch Pharmacol 2011; 384:439-49. [PMID: 21394481 DOI: 10.1007/s00210-011-0619-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Accepted: 02/26/2011] [Indexed: 01/31/2023]
Abstract
After the recent report of the expression of several nme genes in the zebrafish gonads, the present study aimed at further analyzing the expression of nme genes in the ovary with special attention for the nme transcripts that are maternally inherited and could thus participate in the determination of oocyte developmental competence. The expression levels of all groups I and II nme genes were characterized by QPCR in a panel of zebrafish tissues. The nme genes exhibiting an ovarian expression were subsequently monitored throughout oogenesis and early development, and their expression sites characterized using in situ hybridization. Here, we show that nme2b1, nme3, nme4, and nme6 are highly expressed in the ovary and present in the zebrafish oocyte throughout oogenesis. While the four transcripts are maternally inherited, nme3 and nme6 display a typical maternal profile and are detected in the zebrafish early embryo. In contrast to nme3, nme6, abundance exhibits a sharp decrease during early embryogenesis. After zygotic genome activation, we observed an increased expression of nme2b1, nme2b2, nme3, and nme6. The present study provides a comprehensive overview of the expression of nme family members during zebrafish oogenesis and early development. In addition, the maternal origin of two nme transcripts in the early embryo is reported here for the first time in any vertebrate species. Together, our observations suggest an important role of the nme family in oocyte and embryo development in vertebrates.
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Affiliation(s)
- T Desvignes
- INRA, UR1037 SCRIBE, Campus de Beaulieu, 35042, Rennes, France
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97
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Pikulkaew S, Benato F, Celeghin A, Zucal C, Skobo T, Colombo L, Dalla Valle L. The knockdown of maternal glucocorticoid receptor mRNA alters embryo development in zebrafish. Dev Dyn 2011; 240:874-89. [PMID: 21360790 DOI: 10.1002/dvdy.22586] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2011] [Indexed: 01/01/2023] Open
Abstract
In zebrafish, ovulated oocytes contain both maternal cortisol and the mRNA for the glucocorticoid receptor (gr), which is spread as granular structures throughout the ooplasm. At 0.2 hpf, this transcript is relocated in the blastodisc area and partitioned among blastomeres. At 6-8 hpf, it is replaced by zygotic transcript. We used morpholinos to block translation of both maternal and zygotic gr transcripts, and a missplicing morpholino to block post-transcriptionally the zygotic transcript alone. Only knockdown of translation produced an increase of apoptosis and subsequent craniofacial and caudal deformities with severe malformations of neural, vascular, and visceral organs in embryos and 5-dpf larvae. Such defects were rescued with trout gr2 mRNA. Microarray analysis revealed that 114 and 37 highly expressed transcripts were up- and down-regulated, respectively, by maternal Gr protein deficiency in 5-hpf embryos. These results indicate that the maternal gr transcript and protein participate in the maternal programming of zebrafish development.
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Affiliation(s)
- S Pikulkaew
- Comparative Endocrinology Laboratory, Department of Biology, University of Padova, Padova, Italy
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98
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Abstract
Due to the powerful combination of genetic and embryological techniques, the teleost fish Danio rerio has emerged in the last decade as an important model organism for the study of embryonic development. It is relatively easy to inject material such as mRNA or synthetic oligonucleotides to reduce or increase the expression of a gene product. Changes in gene expression can be analyzed at the level of mRNA, by whole-mount in situ hybridization, or at the level of protein, by immunofluorescence. It is also possible to quantitatively analyze protein levels by Western and immunoprecipitation. Cell behavior can be analyzed in detail by cell transplantation and by fate mapping. Because a large number of mutations have been identified in recent years, these methods can be applied in a variety of contexts to provide a deep understanding of gene function that is often more difficult to achieve in other vertebrate model systems.
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Affiliation(s)
- Yuhua Sun
- Department of Cellular Biology, The University of Georgia, Athens, GA, USA.
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99
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Gallenberger M, Meinel DM, Kroeber M, Wegner M, Milkereit P, Bösl MR, Tamm ER. Lack of WDR36 leads to preimplantation embryonic lethality in mice and delays the formation of small subunit ribosomal RNA in human cells in vitro. Hum Mol Genet 2010; 20:422-35. [DOI: 10.1093/hmg/ddq478] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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100
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brca2 in zebrafish ovarian development, spermatogenesis, and tumorigenesis. Proc Natl Acad Sci U S A 2010; 107:19350-5. [PMID: 20974951 DOI: 10.1073/pnas.1011630107] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Humans with inherited mutations in BRCA2 are at increased risk for developing breast and ovarian cancer; however, the relationship between BRCA2 mutation and these cancers is not understood. Studies of Brca2 mutation by gene targeting in mice are limited, given that homozygous Brca2 mutation typically leads to early embryonic lethality. We established a zebrafish line with a nonsense mutation in brca2 exon 11 (brca2(Q658X)), a mutation similar in location and type to BRCA2 mutations found in humans with hereditary breast and ovarian cancer. brca2(Q658X) homozygous zebrafish are viable and survive to adulthood; however, juvenile homozygotes fail to develop ovaries during sexual differentiation. Instead, brca2(Q658X) homozygotes develop as infertile males with meiotic arrest in spermatocytes. Germ cell migration to the embryonic gonadal ridge is unimpaired in brca2(Q658X) homozygotes; thus, failure of ovarian development is not due to defects in early establishment of the embryonic gonad. Homozygous tp53 mutation rescues ovarian development in brca2(Q658X) homozygous zebrafish, reflecting the importance of germ cell apoptosis in gonad morphogenesis. Adult brca2(Q658X) homozygous zebrafish are predisposed to testicular neoplasias. In addition, tumorigenesis in multiple tissues is significantly accelerated in combination with homozygous tp53 mutation in both brca2(Q658X) homozygous and brca2(Q658X) heterozygous zebrafish. These studies reveal critical roles for brca2 in ovarian development and tumorigenesis in reproductive tissues.
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