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Roos FJM, van Tienderen GS, Wu H, Bordeu I, Vinke D, Albarinos LM, Monfils K, Niesten S, Smits R, Willemse J, Rosmark O, Westergren-Thorsson G, Kunz DJ, de Wit M, French PJ, Vallier L, IJzermans JNM, Bartfai R, Marks H, Simons BD, van Royen ME, Verstegen MMA, van der Laan LJW. Human branching cholangiocyte organoids recapitulate functional bile duct formation. Cell Stem Cell 2022; 29:776-794.e13. [PMID: 35523140 DOI: 10.1016/j.stem.2022.04.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 02/25/2022] [Accepted: 04/14/2022] [Indexed: 12/13/2022]
Abstract
Human cholangiocyte organoids show great promise for regenerative therapies and in vitro modeling of bile duct development and diseases. However, the cystic organoids lack the branching morphology of intrahepatic bile ducts (IHBDs). Here, we report establishing human branching cholangiocyte organoid (BRCO) cultures. BRCOs self-organize into complex tubular structures resembling the IHBD architecture. Single-cell transcriptomics and functional analysis showed high similarity to primary cholangiocytes, and importantly, the branching growth mimics aspects of tubular development and is dependent on JAG1/NOTCH2 signaling. When applied to cholangiocarcinoma tumor organoids, the morphology changes to an in vitro morphology like primary tumors. Moreover, these branching cholangiocarcinoma organoids (BRCCAOs) better match the transcriptomic profile of primary tumors and showed increased chemoresistance to gemcitabine and cisplatin. In conclusion, BRCOs recapitulate a complex process of branching morphogenesis in vitro. This provides an improved model to study tubular formation, bile duct functionality, and associated biliary diseases.
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Affiliation(s)
- Floris J M Roos
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Gilles S van Tienderen
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Haoyu Wu
- Radboud University, Department of Molecular Biology, Nijmegen, the Netherlands
| | - Ignacio Bordeu
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Dina Vinke
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Laura Muñoz Albarinos
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Kathryn Monfils
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Sabrah Niesten
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Ron Smits
- Erasmus MC, University Medical Center Rotterdam, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands
| | - Jorke Willemse
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Oskar Rosmark
- Lung Biology, Department Experimental Medical Science, Lund University, Lund, Sweden
| | | | - Daniel J Kunz
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, University of Cambridge, Cambridge, UK
| | - Maurice de Wit
- Erasmus MC, University Medical Center Rotterdam, Department of Pathology, Rotterdam, the Netherlands
| | - Pim J French
- Erasmus MC, University Medical Center Rotterdam, Cancer Treatment Screening Facility, Department of Neurology, Rotterdam, the Netherlands
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Jan N M IJzermans
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Richard Bartfai
- Radboud University, Department of Molecular Biology, Nijmegen, the Netherlands
| | - Hendrik Marks
- Radboud University, Department of Molecular Biology, Nijmegen, the Netherlands
| | - Ben D Simons
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK; Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Martin E van Royen
- Erasmus MC, University Medical Center Rotterdam, Department of Pathology, Rotterdam, the Netherlands
| | - Monique M A Verstegen
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands
| | - Luc J W van der Laan
- Erasmus MC Transplant Institute, University Medical Center Rotterdam, Department of Surgery, Rotterdam, the Netherlands.
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Abstract
BACKGROUND Despite the popularity of zebrafish as a research model, its sex determination (SD) mechanism is still unknown. Most cytogenetic studies failed to find dimorphic sex chromosomes and no primary sex determining switch has been identified even though the assembly of zebrafish genome sequence is near to completion and a high resolution genetic map is available. Recent publications suggest that environmental factors within the natural range have minimal impact on sex ratios of zebrafish populations. The primary aim of this study is to find out more about how sex is determined in zebrafish. METHODOLOGY/PRINCIPAL FINDINGS Using classical breeding experiments, we found that sex ratios across families were wide ranging (4.8% to 97.3% males). On the other hand, repeated single pair crossings produced broods of very similar sex ratios, indicating that parental genotypes have a role in the sex ratio of the offspring. Variation among family sex ratios was reduced after selection for breeding pairs with predominantly male or female offspring, another indication that zebrafish sex is regulated genetically. Further examinations by a PCR-based "blind assay" and array comparative genomic hybridization both failed to find universal sex-linked differences between the male and female genomes. Together with the ability to increase the sex bias of lines by selective breeding, these data suggest that zebrafish is unlikely to utilize a chromosomal sex determination (CSD) system. CONCLUSIONS/SIGNIFICANCE Taken together, our study suggests that zebrafish sex is genetically determined with limited, secondary influences from the environment. As we have not found any sign for CSD in the species, we propose that the zebrafish has a polygenic sex determination system.
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Affiliation(s)
- Woei Chang Liew
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Richard Bartfai
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Zijie Lim
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Rajini Sreenivasan
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Kellee R. Siegfried
- Department of Genetics, Max-Planck-Institut für Entwicklungsbiologie, Tübingen, Germany
| | - Laszlo Orban
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Department of Animal Sciences and Animal Husbandry, University of Pannonia, Keszthely, Hungary
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Laurentino EC, Taylor S, Mair GR, Lasonder E, Bartfai R, Stunnenberg HG, Kroeze H, Ramesar J, Franke-Fayard B, Khan SM, Janse CJ, Waters AP. Experimentally controlled downregulation of the histone chaperone FACT in Plasmodium berghei reveals that it is critical to male gamete fertility. Cell Microbiol 2011; 13:1956-74. [PMID: 21899698 PMCID: PMC3429858 DOI: 10.1111/j.1462-5822.2011.01683.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human FACT (facilitates chromatin transcription) consists of the proteins SPT16 and SSRP1 and acts as a histone chaperone in the (dis)assembly of nucleosome (and thereby chromatin) structure during transcription and DNA replication. We identified a Plasmodium berghei protein, termed FACT-L, with homology to the SPT16 subunit of FACT. Epitope tagging of FACT-L showed nuclear localization with high expression in the nuclei of (activated) male gametocytes. The gene encoding FACT-L could not be deleted indicating an essential role during blood-stage development. Using a ‘promoter-swap’ approach whereby the fact-l promoter was replaced by an ‘asexual blood stage-specific’ promoter that is silent in gametocytes, transcription of fact-l in promoter-swap mutant gametocytes was downregulated compared with wild-type gametocytes. These mutant male gametocytes showed delayed DNA replication and gamete formation. Male gamete fertility was strongly reduced while female gamete fertility was unaffected; residual ookinetes generated oocysts that arrested early in development and failed to enter sporogony. Therefore FACT is critically involved in the formation of fertile male gametes and parasite transmission. ‘Promoter swapping’ is a powerful approach for the functional analysis of proteins in gametocytes (and beyond) that are essential during asexual blood-stage development.
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Affiliation(s)
- Eliane C Laurentino
- Leiden Malaria Research Group, Department of Parasitology, Leiden University Medical, Albinusdreef 2, 2333 ZA Leiden, the Netherlands
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Richard D, Bartfai R, Volz J, Ralph SA, Muller S, Stunnenberg HG, Cowman AF. A genome-wide chromatin-associated nuclear peroxiredoxin from the malaria parasite Plasmodium falciparum. J Biol Chem 2011; 286:11746-55. [PMID: 21282103 PMCID: PMC3064226 DOI: 10.1074/jbc.m110.198499] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 01/13/2011] [Indexed: 11/16/2022] Open
Abstract
Malaria parasites are subjected to high levels of oxidative stress during their development inside erythrocytes and the ability of the parasite to defend itself against this assault is critical to its survival. Therefore, Plasmodium possesses an effective antioxidant defense system that could potentially be used as a target for the development of inhibitor-based therapy. We have identified an unusual peroxiredoxin protein that localizes to the nucleus of Plasmodium falciparum and have renamed it PfnPrx (PF10_0268, earlier called MCP1). Our work reveals that PfnPrx has a broad specificity of substrate being able to utilize thioredoxin and glutaredoxin as reductants and having the ability to reduce simple and complex peroxides. Intriguingly, chromatin immunoprecipitation followed by deep sequencing reveals that the enzyme associates with chromatin in a genome-wide manner with a slight enrichment in coding regions. Our results represent the first description of a dedicated chromatin-associated peroxiredoxin and potentially represent an ingenious way by which the parasite can survive the highly oxidative environment within its human host.
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Affiliation(s)
- Dave Richard
- From The Walter and Eliza Hall Institute of Medical Research, Melbourne 3052, Australia
| | - Richard Bartfai
- the Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen 6525 GA, The Netherlands
| | - Jennifer Volz
- From The Walter and Eliza Hall Institute of Medical Research, Melbourne 3052, Australia
| | - Stuart A. Ralph
- the Bio21 Molecular Sciences and Biotechnology Institute, University of Melbourne, Melbourne 3052, Australia
| | - Sylke Muller
- the Division of Infection & Immunity and Wellcome Centre for Parasitology, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom, and
| | - Hendrik G. Stunnenberg
- the Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen 6525 GA, The Netherlands
| | - Alan F. Cowman
- From The Walter and Eliza Hall Institute of Medical Research, Melbourne 3052, Australia
- the Department of Medical Biology, University of Melbourne, Melbourne 3052, Australia
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Li Y, Chia JM, Bartfai R, Christoffels A, Yue GH, Ding K, Ho MY, Hill JA, Stupka E, Orban L. Comparative analysis of the testis and ovary transcriptomes in zebrafish by combining experimental and computational tools. Comp Funct Genomics 2010; 5:403-18. [PMID: 18629171 PMCID: PMC2447462 DOI: 10.1002/cfg.418] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2004] [Revised: 06/25/2004] [Accepted: 06/28/2004] [Indexed: 11/12/2022] Open
Abstract
Studies on the zebrafish model have contributed to our understanding of several important developmental processes, especially those that can be easily studied in the embryo. However, our knowledge on late events such as gonad differentiation in the zebrafish is still limited. Here we provide an analysis on the gene sets expressed in the adult zebrafish testis and ovary in an attempt to identify genes with potential role in (zebra)fish gonad development and function. We produced 10,533 expressed sequence tags (ESTs) from zebrafish testis or ovary and downloaded an additional 23,642 gonad-derived sequences from the zebrafish EST database. We clustered these sequences together with over 13,000 kidney-derived zebrafish ESTs to study partial transcriptomes for these three organs. We searched for genes with gonad-specific expression by screening macroarrays containing at least 2600 unique cDNA inserts with testis-, ovary- and kidney-derived cDNA probes. Clones hybridizing to only one of the two gonad probes were selected, and subsequently screened with computational tools to identify 72 genes with potentially testis-specific and 97 genes with potentially ovary-specific expression, respectively. PCR-amplification confirmed gonad-specificity for 21 of the 45 clones tested (all without known function). Our study, which involves over 47,000 EST sequences and specialized cDNA arrays, is the first analysis of adult organ transcriptomes of zebrafish at such a scale. The study of genes expressed in adult zebrafish testis and ovary will provide useful information on regulation of gene expression in teleost gonads and might also contribute to our understanding of the development and differentiation of reproductive organs in vertebrates.
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Affiliation(s)
- Yang Li
- Reproductive Genomics Group, Temasek Lifesciences Laboratory, Singapore
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Flueck C, Bartfai R, Niederwieser I, Witmer K, Alako BTF, Moes S, Bozdech Z, Jenoe P, Stunnenberg HG, Voss TS. A major role for the Plasmodium falciparum ApiAP2 protein PfSIP2 in chromosome end biology. PLoS Pathog 2010; 6:e1000784. [PMID: 20195509 PMCID: PMC2829057 DOI: 10.1371/journal.ppat.1000784] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 01/20/2010] [Indexed: 12/30/2022] Open
Abstract
The heterochromatic environment and physical clustering of chromosome ends at the nuclear periphery provide a functional and structural framework for antigenic variation and evolution of subtelomeric virulence gene families in the malaria parasite Plasmodium falciparum. While recent studies assigned important roles for reversible histone modifications, silent information regulator 2 and heterochromatin protein 1 (PfHP1) in epigenetic control of variegated expression, factors involved in the recruitment and organization of subtelomeric heterochromatin remain unknown. Here, we describe the purification and characterization of PfSIP2, a member of the ApiAP2 family of putative transcription factors, as the unknown nuclear factor interacting specifically with cis-acting SPE2 motif arrays in subtelomeric domains. Interestingly, SPE2 is not bound by the full-length protein but rather by a 60kDa N-terminal domain, PfSIP2-N, which is released during schizogony. Our experimental re-definition of the SPE2/PfSIP2-N interaction highlights the strict requirement of both adjacent AP2 domains and a conserved bipartite SPE2 consensus motif for high-affinity binding. Genome-wide in silico mapping identified 777 putative binding sites, 94% of which cluster in heterochromatic domains upstream of subtelomeric var genes and in telomere-associated repeat elements. Immunofluorescence and chromatin immunoprecipitation (ChIP) assays revealed co-localization of PfSIP2-N with PfHP1 at chromosome ends. Genome-wide ChIP demonstrated the exclusive binding of PfSIP2-N to subtelomeric SPE2 landmarks in vivo but not to single chromosome-internal sites. Consistent with this specialized distribution pattern, PfSIP2-N over-expression has no effect on global gene transcription. Hence, contrary to the previously proposed role for this factor in gene activation, our results provide strong evidence for the first time for the involvement of an ApiAP2 factor in heterochromatin formation and genome integrity. These findings are highly relevant for our understanding of chromosome end biology and variegated expression in P. falciparum and other eukaryotes, and for the future analysis of the role of ApiAP2-DNA interactions in parasite biology.
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Affiliation(s)
- Christian Flueck
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, University of Basel, Basel, Switzerland
| | - Richard Bartfai
- Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Igor Niederwieser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, University of Basel, Basel, Switzerland
| | - Kathrin Witmer
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, University of Basel, Basel, Switzerland
| | - Blaise T. F. Alako
- Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Suzette Moes
- Biozentrum, University of Basel, Basel, Switzerland
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Paul Jenoe
- Biozentrum, University of Basel, Basel, Switzerland
| | - Hendrik G. Stunnenberg
- Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Till S. Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, University of Basel, Basel, Switzerland
- * E-mail:
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Flueck C, Bartfai R, Volz J, Niederwieser I, Salcedo-Amaya AM, Alako BTF, Ehlgen F, Ralph SA, Cowman AF, Bozdech Z, Stunnenberg HG, Voss TS. Plasmodium falciparum heterochromatin protein 1 marks genomic loci linked to phenotypic variation of exported virulence factors. PLoS Pathog 2009; 5:e1000569. [PMID: 19730695 PMCID: PMC2731224 DOI: 10.1371/journal.ppat.1000569] [Citation(s) in RCA: 217] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 08/07/2009] [Indexed: 02/01/2023] Open
Abstract
Epigenetic processes are the main conductors of phenotypic variation in eukaryotes. The malaria parasite Plasmodium falciparum employs antigenic variation of the major surface antigen PfEMP1, encoded by 60 var genes, to evade acquired immune responses. Antigenic variation of PfEMP1 occurs through in situ switches in mono-allelic var gene transcription, which is PfSIR2-dependent and associated with the presence of repressive H3K9me3 marks at silenced loci. Here, we show that P. falciparum heterochromatin protein 1 (PfHP1) binds specifically to H3K9me3 but not to other repressive histone methyl marks. Based on nuclear fractionation and detailed immuno-localization assays, PfHP1 constitutes a major component of heterochromatin in perinuclear chromosome end clusters. High-resolution genome-wide chromatin immuno-precipitation demonstrates the striking association of PfHP1 with virulence gene arrays in subtelomeric and chromosome-internal islands and a high correlation with previously mapped H3K9me3 marks. These include not only var genes, but also the majority of P. falciparum lineage-specific gene families coding for exported proteins involved in host-parasite interactions. In addition, we identified a number of PfHP1-bound genes that were not enriched in H3K9me3, many of which code for proteins expressed during invasion or at different life cycle stages. Interestingly, PfHP1 is absent from centromeric regions, implying important differences in centromere biology between P. falciparum and its human host. Over-expression of PfHP1 results in an enhancement of variegated expression and highlights the presence of well-defined heterochromatic boundaries. In summary, we identify PfHP1 as a major effector of virulence gene silencing and phenotypic variation. Our results are instrumental for our understanding of this widely used survival strategy in unicellular pathogens.
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Affiliation(s)
- Christian Flueck
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Basle, Switzerland
| | - Richard Bartfai
- Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Jennifer Volz
- Division of Infection and Immunity, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Igor Niederwieser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Basle, Switzerland
| | - Adriana M. Salcedo-Amaya
- Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Blaise T. F. Alako
- Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Florian Ehlgen
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Stuart A. Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia
| | - Alan F. Cowman
- Division of Infection and Immunity, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Hendrik G. Stunnenberg
- Department of Molecular Biology, Nijmegen Center of Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Till S. Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical Institute, Basle, Switzerland
- * E-mail:
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Sreenivasan R, Wang X, Bartfai R, Kwan HY, Christoffels A, Orban L. Global Expression Profiling in Zebrafish Reveals Genes with Potential Roles in Sexual Differentiation. Biol Reprod 2008. [DOI: 10.1093/biolreprod/78.s1.116b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Sreenivasan R, Cai M, Bartfai R, Wang X, Christoffels A, Orban L. Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain. PLoS One 2008; 3:e1791. [PMID: 18335061 PMCID: PMC2262149 DOI: 10.1371/journal.pone.0001791] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Accepted: 02/07/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Our knowledge on zebrafish reproduction is very limited. We generated a gonad-derived cDNA microarray from zebrafish and used it to analyze large-scale gene expression profiles in adult gonads and other organs. METHODOLOGY/PRINCIPAL FINDINGS We have identified 116638 gonad-derived zebrafish expressed sequence tags (ESTs), 21% of which were isolated in our lab. Following in silico normalization, we constructed a gonad-derived microarray comprising 6370 unique, full-length cDNAs from differentiating and adult gonads. Labeled targets from adult gonad, brain, kidney and 'rest-of-body' from both sexes were hybridized onto the microarray. Our analyses revealed 1366, 881 and 656 differentially expressed transcripts (34.7% novel) that showed highest expression in ovary, testis and both gonads respectively. Hierarchical clustering showed correlation of the two gonadal transcriptomes and their similarities to those of the brains. In addition, we have identified 276 genes showing sexually dimorphic expression both between the brains and between the gonads. By in situ hybridization, we showed that the gonadal transcripts with the strongest array signal intensities were germline-expressed. We found that five members of the GTP-binding septin gene family, from which only one member (septin 4) has previously been implicated in reproduction in mice, were all strongly expressed in the gonads. CONCLUSIONS/SIGNIFICANCE We have generated a gonad-derived zebrafish cDNA microarray and demonstrated its usefulness in identifying genes with sexually dimorphic co-expression in both the gonads and the brains. We have also provided the first evidence of large-scale differential gene expression between female and male brains of a teleost. Our microarray would be useful for studying gonad development, differentiation and function not only in zebrafish but also in related teleosts via cross-species hybridizations. Since several genes have been shown to play similar roles in gonadogenesis in zebrafish and other vertebrates, our array may even provide information on genetic disorders affecting gonadal phenotypes and fertility in mammals.
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Affiliation(s)
- Rajini Sreenivasan
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Minnie Cai
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Richard Bartfai
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
| | - Xingang Wang
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Alan Christoffels
- Computational Biology, Temasek Life Sciences Laboratory, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Laszlo Orban
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- * To whom correspondence should be addressed. E-mail:
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Christoffels A, Bartfai R, Srinivasan H, Komen H, Orban L. Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome. BMC Bioinformatics 2006; 7 Suppl 5:S2. [PMID: 17254304 PMCID: PMC1764476 DOI: 10.1186/1471-2105-7-s5-s2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background Automatic annotation of sequenced eukaryotic genomes integrates a combination of methodologies such as ab-initio methods and alignment of homologous genes and/or proteins. For example, annotation of the zebrafish genome within Ensembl relies heavily on available cDNA and protein sequences from two distantly related fish species and other vertebrates that have diverged several hundred million years ago. The scarcity of genomic information from other cyprinids provides the impetus to leverage EST collections to understand gene structures in this diverse teleost group. Results We have generated 6,050 ESTs from the differentiating testis of common carp (Cyprinus carpio) and clustered them with 9,303 non-gonadal ESTs from CarpBase as well as 1,317 ESTs and 652 common carp mRNAs from GenBank. Over 28% of the resulting 8,663 unique transcripts are exclusively testis-derived ESTs. Moreover, 974 of these transcripts did not match any sequence in the zebrafish or fathead minnow EST collection. A total of 1,843 unique common carp sequences could be stringently mapped to the zebrafish genome (version 5), of which 1,752 matched coding sequences of zebrafish genes with or without potential splice variants. We show that 91 common carp transcripts map to intergenic and intronic regions on the zebrafish genome assembly and regions annotated with non-teleost sequences. Interestingly, an additional 42 common carp transcripts indicate the potential presence of new splicing variants not found in zebrafish databases so far. The fact that common carp transcripts help the identification or confirmation of these coding regions in zebrafish exemplifies the usefulness of sequences from closely related species for the annotation of model genomes. We also demonstrate that 5' UTR sequences of common carp and zebrafish orthologs share a significant level of similarity based on preservation of motif arrangements for as many as 10 ab-initio motifs. Conclusion Our data show that there is sufficient homology between the transcribed sequences of common carp and zebrafish to warrant an even deeper cyprinid transcriptome comparison. On the other hand, the comparative analysis illustrates the value in utilizing partially sequenced transcriptomes to understand gene structure in this diverse teleost group. We highlight the need for integrated resources to leverage the wealth of fragmented genomic data.
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Affiliation(s)
- Alan Christoffels
- Computational Biology Group, Temasek Life Sciences Laboratory, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Richard Bartfai
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
| | - Hamsa Srinivasan
- Computational Biology Group, Temasek Life Sciences Laboratory, Singapore
| | - Hans Komen
- Animal Breeding and Genetics Group, Wageningen University, Wageningen, The Netherlands
| | - Laszlo Orban
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore
- Department of Biological Sciences, The National University of Singapore, Singapore
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