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Lardenois A, Gattiker A, Collin O, Chalmel F, Primig M. GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2010; 2010:baq030. [PMID: 21149299 PMCID: PMC3004465 DOI: 10.1093/database/baq030] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
GermOnline 4.0 is a cross-species database portal focusing on high-throughput expression data relevant for germline development, the meiotic cell cycle and mitosis in healthy versus malignant cells. It is thus a source of information for life scientists as well as clinicians who are interested in gene expression and regulatory networks. The GermOnline gateway provides unlimited access to information produced with high-density oligonucleotide microarrays (3'-UTR GeneChips), genome-wide protein-DNA binding assays and protein-protein interaction studies in the context of Ensembl genome annotation. Samples used to produce high-throughput expression data and to carry out genome-wide in vivo DNA binding assays are annotated via the MIAME-compliant Multiomics Information Management and Annotation System (MIMAS 3.0). Furthermore, the Saccharomyces Genomics Viewer (SGV) was developed and integrated into the gateway. SGV is a visualization tool that outputs genome annotation and DNA-strand specific expression data produced with high-density oligonucleotide tiling microarrays (Sc_tlg GeneChips) which cover the complete budding yeast genome on both DNA strands. It facilitates the interpretation of expression levels and transcript structures determined for various cell types cultured under different growth and differentiation conditions. Database URL: www.germonline.org/
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Affiliation(s)
- Aurélie Lardenois
- Inserm, U625, GERHM, IFR-140, Université de Rennes 1, F-35042 Rennes, France
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Roy Choudhury D, Small C, Wang Y, Mueller PR, Rebel VI, Griswold MD, McCarrey JR. Microarray-based analysis of cell-cycle gene expression during spermatogenesis in the mouse. Biol Reprod 2010; 83:663-75. [PMID: 20631398 DOI: 10.1095/biolreprod.110.084889] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Mammalian spermatogenesis is a continuum of cellular differentiation in a lineage that features three principal stages: 1) a mitotically active stage in spermatogonia, 2) a meiotic stage in spermatocytes, and 3) a postreplicative stage in spermatids. We used a microarray-based approach to identify changes in expression of cell-cycle genes that distinguish 1) mitotic type A spermatogonia from meiotic pachytene spermatocytes and 2) pachytene spermatocytes from postreplicative round spermatids. We detected expression of 550 genes related to cell-cycle function in one or more of these cell types. Although a majority of these genes were expressed during all three stages of spermatogenesis, we observed dramatic changes in levels of individual transcripts between mitotic spermatogonia and meiotic spermatocytes and between meiotic spermatocytes and postreplicative spermatids. Our results suggest that distinct cell-cycle gene regulatory networks or subnetworks are associated with each phase of the cell cycle in each spermatogenic cell type. In addition, we observed expression of different members of certain cell-cycle gene families in each of the three spermatogenic cell types investigated. Finally, we report expression of 221 cell-cycle genes that have not previously been annotated as part of the cell cycle network expressed during spermatogenesis, including eight novel genes that appear to be testis-specific.
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Screening of Chicken Genes Related to Germ Cell Development. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2007. [DOI: 10.5187/jast.2007.49.2.183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Wyrobek AJ, Mulvihill JJ, Wassom JS, Malling HV, Shelby MD, Lewis SE, Witt KL, Preston RJ, Perreault SD, Allen JW, DeMarini DM, Woychik RP, Bishop JB. Assessing human germ-cell mutagenesis in the Postgenome Era: a celebration of the legacy of William Lawson (Bill) Russell. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2007; 48:71-95. [PMID: 17295306 PMCID: PMC2071946 DOI: 10.1002/em.20284] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Birth defects, de novo genetic diseases, and chromosomal abnormality syndromes occur in approximately 5% of all live births, and affected children suffer from a broad range of lifelong health consequences. Despite the social and medical impact of these defects, and the 8 decades of research in animal systems that have identified numerous germ-cell mutagens, no human germ-cell mutagen has been confirmed to date. There is now a growing consensus that the inability to detect human germ-cell mutagens is due to technological limitations in the detection of random mutations rather than biological differences between animal and human susceptibility. A multidisciplinary workshop responding to this challenge convened at The Jackson Laboratory in Bar Harbor, Maine. The purpose of the workshop was to assess the applicability of an emerging repertoire of genomic technologies to studies of human germ-cell mutagenesis. Workshop participants recommended large-scale human germ-cell mutation studies be conducted using samples from donors with high-dose exposures, such as cancer survivors. Within this high-risk cohort, parents and children could be evaluated for heritable changes in (a) DNA sequence and chromosomal structure, (b) repeat sequences and minisatellites, and (c) global gene expression profiles and pathways. Participants also advocated the establishment of a bio-bank of human tissue samples from donors with well-characterized exposure, including medical and reproductive histories. This mutational resource could support large-scale, multiple-endpoint studies. Additional studies could involve the examination of transgenerational effects associated with changes in imprinting and methylation patterns, nucleotide repeats, and mitochondrial DNA mutations. The further development of animal models and the integration of these with human studies are necessary to provide molecular insights into the mechanisms of germ-cell mutations and to identify prevention strategies. Furthermore, scientific specialty groups should be convened to review and prioritize the evidence for germ-cell mutagenicity from common environmental, occupational, medical, and lifestyle exposures. Workshop attendees agreed on the need for a full-scale assault to address key fundamental questions in human germ-cell environmental mutagenesis. These include, but are not limited to, the following: Do human germ-cell mutagens exist? What are the risks to future generations? Are some parents at higher risk than others for acquiring and transmitting germ-cell mutations? Obtaining answers to these, and other critical questions, will require strong support from relevant funding agencies, in addition to the engagement of scientists outside the fields of genomics and germ-cell mutagenesis.
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Affiliation(s)
| | - John J. Mulvihill
- University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - John S. Wassom
- YAHSGS, LLC, Richland, Washington
- Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Heinrich V. Malling
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Michael D. Shelby
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | | | - Kristine L. Witt
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - R. Julian Preston
- US Environmental Protection Agency, Research Triangle Park, North Carolina
| | - Sally D. Perreault
- US Environmental Protection Agency, Research Triangle Park, North Carolina
| | - James W. Allen
- US Environmental Protection Agency, Research Triangle Park, North Carolina
| | - David M. DeMarini
- US Environmental Protection Agency, Research Triangle Park, North Carolina
| | | | - Jack B. Bishop
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
- *Correspondence to: Dr. Jack B. Bishop, National Institute of Environmental Health Sciences, EC-01, PO Box 12233, Research Triangle Park, North Carolina, USA. E-mail:
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Gattiker A, Niederhauser-Wiederkehr C, Moore J, Hermida L, Primig M. The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction. Nucleic Acids Res 2006; 35:D457-62. [PMID: 17145711 PMCID: PMC1751528 DOI: 10.1093/nar/gkl957] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report a novel release of the GermOnline knowledgebase covering genes relevant for the cell cycle, gametogenesis and fertility. GermOnline was extended into a cross-species systems browser including information on DNA sequence annotation, gene expression and the function of gene products. The database covers eight model organisms and Homo sapiens, for which complete genome annotation data are available. The database is now built around a sophisticated genome browser (Ensembl), our own microarray information management and annotation system (MIMAS) used to extensively describe experimental data obtained with high-density oligonucleotide microarrays (GeneChips) and a comprehensive system for online editing of database entries (MediaWiki). The RNA data include results from classical microarrays as well as tiling arrays that yield information on RNA expression levels, transcript start sites and lengths as well as exon composition. Members of the research community are solicited to help GermOnline curators keep database entries on genes and gene products complete and accurate. The database is accessible at .
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Affiliation(s)
| | | | | | | | - Michael Primig
- To whom correspondence should be addressed. Tel: +41 61 267 2098; Fax: +41 61 267 3398;
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Hochwagen A, Wrobel G, Cartron M, Demougin P, Niederhauser-Wiederkehr C, Boselli MG, Primig M, Amon A. Novel response to microtubule perturbation in meiosis. Mol Cell Biol 2005; 25:4767-81. [PMID: 15899877 PMCID: PMC1140642 DOI: 10.1128/mcb.25.11.4767-4781.2005] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During the mitotic cell cycle, microtubule depolymerization leads to a cell cycle arrest in metaphase, due to activation of the spindle checkpoint. Here, we show that under microtubule-destabilizing conditions, such as low temperature or the presence of the spindle-depolymerizing drug benomyl, meiotic budding yeast cells arrest in G(1) or G(2), instead of metaphase. Cells arrest in G(1) if microtubule perturbation occurs as they enter the meiotic cell cycle and in G(2) if cells are already undergoing premeiotic S phase. Concomitantly, cells down-regulate genes required for cell cycle progression, meiotic differentiation, and spore formation in a highly coordinated manner. Decreased expression of these genes is likely to be responsible for halting both cell cycle progression and meiotic development. Our results point towards the existence of a novel surveillance mechanism of microtubule integrity that may be particularly important during specialized cell cycles when coordination of cell cycle progression with a developmental program is necessary.
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Affiliation(s)
- Andreas Hochwagen
- Center for Cancer Research, Howard Hughes Medical Institute, Massachusetts Institute of Technology, E17-233, 40 Ames St., Cambridge, MA 02139, USA
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Hermida L, Brachat S, Voegeli S, Philippsen P, Primig M. The Ashbya Genome Database (AGD)--a tool for the yeast community and genome biologists. Nucleic Acids Res 2005; 33:D348-52. [PMID: 15608214 PMCID: PMC539963 DOI: 10.1093/nar/gki009] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The Ashbya Genome Database (AGD) is a comprehensive online source of information covering genes from the filamentous fungus Ashbya gossypii. The database content is based upon comparative genome annotation between A.gossypii and the closely related budding yeast Saccharomyces cerevisiae taking both sequence similarity and synteny (conserved order and orientation) into account. Release 2 of AGD contains 4718 protein-encoding loci located across seven chromosomes. Information can be retrieved using systematic or standard locus names from A.gossypii as well as budding and fission yeast. Approximately 90% of the genes in the genome of A.gossypii are homologous and syntenic to loci of budding yeast. Therefore, AGD is a useful tool not only for the various yeast communities in general but also for biologists who are interested in evolutionary aspects of genome research and comparative genome annotation. The database provides scientists with a convenient graphical user interface that includes various locus search and genome browsing options, data download and export functionalities and numerous reciprocal links to external databases including SGD, MIPS, GeneDB, KEGG, GermOnline and Swiss-Prot/TrEMBL. AGD is accessible at http://agd.unibas.ch/.
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Affiliation(s)
- Leandro Hermida
- Department of Applied Microbiology, Biozentrum, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland
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Wrobel G, Primig M. Mammalian male germ cells are fertile ground for expression profiling of sexual reproduction. Reproduction 2005; 129:1-7. [PMID: 15615893 DOI: 10.1530/rep.1.00408] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent large-scale transcriptional profiling experiments of mammalian spermatogenesis using rodent model systems and different types of microarrays have yielded insight into the expression program of male germ cells. These studies revealed that an astonishingly large number of loci are differentially expressed during spermatogenesis. Among them are several hundred transcripts that appear to be specific for meiotic and post-meiotic germ cells. This group includes many genes that were previously implicated in spermatogenesis and/or fertility and others that are as yet poorly characterized. Profiling experiments thus reveal candidates for regulation of spermatogenesis and fertility as well as targets for innovative contraceptives that act on gene products absent in somatic tissues. In this review, consolidated high density oligonucleotide microarray data from rodent total testis and purified germ cell samples are analyzed and their impact on our understanding of the transcriptional program governing male germ cell differentiation is discussed.
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Affiliation(s)
- Gunnar Wrobel
- Biozentrum and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
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Schlecht U, Demougin P, Koch R, Hermida L, Wiederkehr C, Descombes P, Pineau C, Jégou B, Primig M. Expression profiling of mammalian male meiosis and gametogenesis identifies novel candidate genes for roles in the regulation of fertility. Mol Biol Cell 2004; 15:1031-43. [PMID: 14718556 PMCID: PMC363067 DOI: 10.1091/mbc.e03-10-0762] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We report a comprehensive large-scale expression profiling analysis of mammalian male germ cells undergoing mitotic growth, meiosis, and gametogenesis by using high-density oligonucleotide microarrays and highly enriched cell populations. Among 11,955 rat loci investigated, 1268 were identified as differentially transcribed in germ cells at subsequent developmental stages compared with total testis, somatic Sertoli cells as well as brain and skeletal muscle controls. The loci were organized into four expression clusters that correspond to somatic, mitotic, meiotic, and postmeiotic cell types. This work provides information about expression patterns of approximately 200 genes known to be important during male germ cell development. Approximately 40 of those are included in a group of 121 transcripts for which we report germ cell expression and lack of transcription in three somatic control cell types. Moreover, we demonstrate the testicular expression and transcriptional induction in mitotic, meiotic, and/or postmeiotic germ cells of 293 as yet uncharacterized transcripts, some of which are likely to encode factors involved in spermatogenesis and fertility. This group also contains potential germ cell-specific targets for innovative contraceptives. A graphical display of the data is conveniently accessible through the GermOnline database at http://www.germonline.org.
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Affiliation(s)
- Ulrich Schlecht
- Biozentrum and Swiss Institute of Bioinformatics, 4056 Basel; Switzerland
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2004. [PMCID: PMC2447433 DOI: 10.1002/cfg.356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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