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Furrer R, Heim B, Schmid S, Dilbaz S, Adak V, Nordström KJV, Ritz D, Steurer SA, Walter J, Handschin C. Molecular control of endurance training adaptation in male mouse skeletal muscle. Nat Metab 2023; 5:2020-2035. [PMID: 37697056 PMCID: PMC10663156 DOI: 10.1038/s42255-023-00891-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/11/2023] [Indexed: 09/13/2023]
Abstract
Skeletal muscle has an enormous plastic potential to adapt to various external and internal perturbations. Although morphological changes in endurance-trained muscles are well described, the molecular underpinnings of training adaptation are poorly understood. We therefore aimed to elucidate the molecular signature of muscles of trained male mice and unravel the training status-dependent responses to an acute bout of exercise. Our results reveal that, even though at baseline an unexpectedly low number of genes define the trained muscle, training status substantially affects the transcriptional response to an acute challenge, both quantitatively and qualitatively, in part associated with epigenetic modifications. Finally, transiently activated factors such as the peroxisome proliferator-activated receptor-γ coactivator 1α are indispensable for normal training adaptation. Together, these results provide a molecular framework of the temporal and training status-dependent exercise response that underpins muscle plasticity in training.
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Affiliation(s)
| | - Barbara Heim
- Biozentrum, University of Basel, Basel, Switzerland
- University Hospital Basel, Basel, Switzerland
| | - Svenia Schmid
- Biozentrum, University of Basel, Basel, Switzerland
- University Hospital Basel, Basel, Switzerland
| | - Sedat Dilbaz
- Biozentrum, University of Basel, Basel, Switzerland
| | - Volkan Adak
- Biozentrum, University of Basel, Basel, Switzerland
| | - Karl J V Nordström
- Laboratory of EpiGenetics, Saarland University, Saarbrücken, Germany
- AstraZeneca, Mölndal, Sweden
| | - Danilo Ritz
- Biozentrum, University of Basel, Basel, Switzerland
| | | | - Jörn Walter
- Laboratory of EpiGenetics, Saarland University, Saarbrücken, Germany
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2
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Petrova V, Song R, Nordström KJV, Walter J, Wong JJL, Armstrong N, Rasko JEJ, Schmitz U. Increased chromatin accessibility facilitates intron retention in specific cell differentiation states. Nucleic Acids Res 2022; 50:11563-11579. [PMID: 36354002 PMCID: PMC9723627 DOI: 10.1093/nar/gkac994] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/05/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022] Open
Abstract
Dynamic intron retention (IR) in vertebrate cells is of widespread biological importance. Aberrant IR is associated with numerous human diseases including several cancers. Despite consistent reports demonstrating that intrinsic sequence features can help introns evade splicing, conflicting findings about cell type- or condition-specific IR regulation by trans-regulatory and epigenetic mechanisms demand an unbiased and systematic analysis of IR in a controlled experimental setting. We integrated matched mRNA sequencing (mRNA-Seq), whole-genome bisulfite sequencing (WGBS), nucleosome occupancy methylome sequencing (NOMe-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) data from primary human myeloid and lymphoid cells. Using these multi-omics data and machine learning, we trained two complementary models to determine the role of epigenetic factors in the regulation of IR in cells of the innate immune system. We show that increased chromatin accessibility, as revealed by nucleosome-free regions, contributes substantially to the retention of introns in a cell-specific manner. We also confirm that intrinsic characteristics of introns are key for them to evade splicing. This study suggests an important role for chromatin architecture in IR regulation. With an increasing appreciation that pathogenic alterations are linked to RNA processing, our findings may provide useful insights for the development of novel therapeutic approaches that target aberrant splicing.
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Affiliation(s)
- Veronika Petrova
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | | | - Karl J V Nordström
- Laboratory of EpiGenetics, Saarland University, Campus A2 4, D-66123 Saarbrücken, Germany
| | - Jörn Walter
- Laboratory of EpiGenetics, Saarland University, Campus A2 4, D-66123 Saarbrücken, Germany
| | - Justin J L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Nicola J Armstrong
- Mathematics and Statistics, Curtin University, Bentley, WA 6102, Australia
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3
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Böhm S, Splith V, Riedmayr LM, Rötzer RD, Gasparoni G, Nordström KJV, Wagner JE, Hinrichsmeyer KS, Walter J, Wahl-Schott C, Fenske S, Biel M, Michalakis S, Becirovic E. A gene therapy for inherited blindness using dCas9-VPR-mediated transcriptional activation. Sci Adv 2020; 6:eaba5614. [PMID: 32875106 PMCID: PMC7438099 DOI: 10.1126/sciadv.aba5614] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/08/2020] [Indexed: 05/08/2023]
Abstract
Catalytically inactive dCas9 fused to transcriptional activators (dCas9-VPR) enables activation of silent genes. Many disease genes have counterparts, which serve similar functions but are expressed in distinct cell types. One attractive option to compensate for the missing function of a defective gene could be to transcriptionally activate its functionally equivalent counterpart via dCas9-VPR. Key challenges of this approach include the delivery of dCas9-VPR, activation efficiency, long-term expression of the target gene, and adverse effects in vivo. Using dual adeno-associated viral vectors expressing split dCas9-VPR, we show efficient transcriptional activation and long-term expression of cone photoreceptor-specific M-opsin (Opn1mw) in a rhodopsin-deficient mouse model for retinitis pigmentosa. One year after treatment, this approach yields improved retinal function and attenuated retinal degeneration with no apparent adverse effects. Our study demonstrates that dCas9-VPR-mediated transcriptional activation of functionally equivalent genes has great potential for the treatment of genetic disorders.
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Affiliation(s)
- Sybille Böhm
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Victoria Splith
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lisa Maria Riedmayr
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - René Dominik Rötzer
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gilles Gasparoni
- Department of Genetics, Saarland University, Saarbrücken, Germany
| | | | - Johanna Elisabeth Wagner
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Klara Sonnie Hinrichsmeyer
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, Saarbrücken, Germany
| | | | - Stefanie Fenske
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin Biel
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stylianos Michalakis
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Ophthalmology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Elvir Becirovic
- Center for Integrated Protein Science Munich CIPSM, Munich, Germany
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
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4
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Nordström KJV, Schmidt F, Gasparoni N, Salhab A, Gasparoni G, Kattler K, Müller F, Ebert P, Costa IG, Pfeifer N, Lengauer T, Schulz MH, Walter J. Unique and assay specific features of NOMe-, ATAC- and DNase I-seq data. Nucleic Acids Res 2020; 47:10580-10596. [PMID: 31584093 PMCID: PMC6847574 DOI: 10.1093/nar/gkz799] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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] [Received: 03/06/2019] [Revised: 08/31/2019] [Accepted: 09/11/2019] [Indexed: 01/01/2023] Open
Abstract
Chromatin accessibility maps are important for the functional interpretation of the genome. Here, we systematically analysed assay specific differences between DNase I-seq, ATAC-seq and NOMe-seq in a side by side experimental and bioinformatic setup. We observe that most prominent nucleosome depleted regions (NDRs, e.g. in promoters) are roboustly called by all three or at least two assays. However, we also find a high proportion of assay specific NDRs that are often ‘called’ by only one of the assays. We show evidence that these assay specific NDRs are indeed genuine open chromatin sites and contribute important information for accurate gene expression prediction. While technically ATAC-seq and DNase I-seq provide a superb high NDR calling rate for relatively low sequencing costs in comparison to NOMe-seq, NOMe-seq singles out for its genome-wide coverage allowing to not only detect NDRs but also endogenous DNA methylation and as we show here genome wide segmentation into heterochromatic B domains and local phasing of nucleosomes outside of NDRs. In summary, our comparisons strongly suggest to consider assay specific differences for the experimental design and for generalized and comparative functional interpretations.
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Affiliation(s)
| | - Florian Schmidt
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.,Excellence Cluster on Multimodal Computing and Interaction, Saarland University, 66123 Saarbrücken, Germany
| | - Nina Gasparoni
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
| | | | - Gilles Gasparoni
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
| | - Kathrin Kattler
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Müller
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Peter Ebert
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University Medical School, 52074 Aachen, Germany
| | | | - Nico Pfeifer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Marcel H Schulz
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.,Excellence Cluster on Multimodal Computing and Interaction, Saarland University, 66123 Saarbrücken, Germany
| | - Jörn Walter
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
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5
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Cheaib M, Dehghani Amirabad A, Nordström KJV, Schulz MH, Simon M. Epigenetic regulation of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia. DNA Res 2015; 22:293-305. [PMID: 26231545 PMCID: PMC4535620 DOI: 10.1093/dnares/dsv014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 06/28/2015] [Indexed: 12/31/2022] Open
Abstract
Phenotypic variation of a single genotype is achieved by alterations in gene expression patterns. Regulation of such alterations depends on their time scale, where short-time adaptations differ from permanently established gene expression patterns maintained by epigenetic mechanisms. In the ciliate Paramecium, serotypes were described for an epigenetically controlled gene expression pattern of an individual multigene family. Paradoxically, individual serotypes can be triggered in Paramecium by alternating environments but are then stabilized by epigenetic mechanisms, thus raising the question to which extend their expression follows environmental stimuli. To characterize environmental adaptation in the context of epigenetically controlled serotype expression, we used RNA-seq to characterize transcriptomes of serotype pure cultures. The resulting vegetative transcriptome resource is first analysed for genes involved in the adaptive response to the altered environment. Secondly, we identified groups of genes that do not follow the adaptive response but show co-regulation with the epigenetically controlled serotype system, suggesting that their gene expression pattern becomes manifested by similar mechanisms. In our experimental set-up, serotype expression and the entire group of co-regulated genes were stable among environmental changes and only heat-shock genes altered expression of these gene groups. The data suggest that the maintenance of these gene expression patterns in a lineage represents epigenetically controlled robustness counteracting short-time adaptation processes.
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Affiliation(s)
- Miriam Cheaib
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken 66123, Germany
| | - Azim Dehghani Amirabad
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken 66123, Germany Cluster of Excellence for Multimodal Computing and Interaction, Saarland University and Max Planck Institute for Informatics, Saarbrücken 66123, Germany
| | - Karl J V Nordström
- Epigenetics Department, Centre for Human and Molecular Biology, Saarland University, Saarbrücken 66123, Germany
| | - Marcel H Schulz
- Cluster of Excellence for Multimodal Computing and Interaction, Saarland University and Max Planck Institute for Informatics, Saarbrücken 66123, Germany
| | - Martin Simon
- Molecular Cell Dynamics, Centre for Human and Molecular Biology, Saarland University, Saarbrücken 66123, Germany
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6
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Willing EM, Rawat V, Mandáková T, Maumus F, James GV, Nordström KJV, Becker C, Warthmann N, Chica C, Szarzynska B, Zytnicki M, Albani MC, Kiefer C, Bergonzi S, Castaings L, Mateos JL, Berns MC, Bujdoso N, Piofczyk T, de Lorenzo L, Barrero-Sicilia C, Mateos I, Piednoël M, Hagmann J, Chen-Min-Tao R, Iglesias-Fernández R, Schuster SC, Alonso-Blanco C, Roudier F, Carbonero P, Paz-Ares J, Davis SJ, Pecinka A, Quesneville H, Colot V, Lysak MA, Weigel D, Coupland G, Schneeberger K. Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nat Plants 2015; 1:14023. [PMID: 27246759 DOI: 10.1038/nplants.2014.23] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/10/2014] [Indexed: 05/10/2023]
Abstract
Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.
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Affiliation(s)
- Eva-Maria Willing
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Vimal Rawat
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Terezie Mandáková
- Research group Plant Cytogenomics, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Florian Maumus
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France
| | - Geo Velikkakam James
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Karl J V Nordström
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Norman Warthmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Claudia Chica
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Bogna Szarzynska
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Matthias Zytnicki
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France
| | - Maria C Albani
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Christiane Kiefer
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Sara Bergonzi
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Loren Castaings
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Julieta L Mateos
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Markus C Berns
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Nora Bujdoso
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Thomas Piofczyk
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Laura de Lorenzo
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Cristina Barrero-Sicilia
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). ETSI agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Isabel Mateos
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Mathieu Piednoël
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Jörg Hagmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Romy Chen-Min-Tao
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). ETSI agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Stephan C Schuster
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Carlos Alonso-Blanco
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Pilar Carbonero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA). ETSI agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Javier Paz-Ares
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, 28049 Madrid, Spain
| | - Seth J Davis
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Ales Pecinka
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Hadi Quesneville
- INRA, UR1164 URGI-Research Unit in Genomics-Info, INRA de Versailles-Grignon, Route de Saint-Cyr, Versailles 78026, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS) UMR 8197 and Institut National de la Santé et de la Recherche Médicale (INSERM) U 1024, Paris, France
| | - Martin A Lysak
- Research group Plant Cytogenomics, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
| | - Korbinian Schneeberger
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, D-50829 Cologne, Germany
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7
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Bergonzi S, Albani MC, Ver Loren van Themaat E, Nordström KJV, Wang R, Schneeberger K, Moerland PD, Coupland G. Mechanisms of age-dependent response to winter temperature in perennial flowering of Arabis alpina. Science 2013; 340:1094-7. [PMID: 23723236 DOI: 10.1126/science.1234116] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Perennial plants live for more than 1 year and flower only after an extended vegetative phase. We used Arabis alpina, a perennial relative of annual Arabidopsis thaliana, to study how increasing age and exposure to winter cold (vernalization) coordinate to establish competence to flower. We show that the APETALA2 transcription factor, a target of microRNA miR172, prevents flowering before vernalization. Additionally, miR156 levels decline as A. alpina ages, causing increased production of SPL (SQUAMOSA PROMOTER BINDING PROTEIN LIKE) transcription factors and ensuring that flowering occurs in response to cold. The age at which plants respond to vernalization can be altered by manipulating miR156 levels. Although miR156 and miR172 levels are uncoupled in A. alpina, miR156 abundance represents the timer controlling age-dependent flowering responses to cold.
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Affiliation(s)
- Sara Bergonzi
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
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8
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James GV, Patel V, Nordström KJV, Klasen JR, Salomé PA, Weigel D, Schneeberger K. User guide for mapping-by-sequencing in Arabidopsis. Genome Biol 2013; 14:R61. [PMID: 23773572 PMCID: PMC3706810 DOI: 10.1186/gb-2013-14-6-r61] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/17/2013] [Indexed: 12/27/2022] Open
Abstract
Mapping-by-sequencing combines genetic mapping with whole-genome sequencing in order to accelerate mutant identification. However, application of mapping-by-sequencing requires decisions on various practical settings on the experimental design that are not intuitively answered. Following an experimentally determined recombination landscape of Arabidopsis and next generation sequencing-specific biases, we simulated more than 400,000 mapping-by-sequencing experiments. This allowed us to evaluate a broad range of different types of experiments and to develop general rules for mapping-by-sequencing in Arabidopsis. Most importantly, this informs about the properties of different crossing scenarios, the number of recombinants and sequencing depth needed for successful mapping experiments.
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9
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Nordström KJV, Albani MC, James GV, Gutjahr C, Hartwig B, Turck F, Paszkowski U, Coupland G, Schneeberger K. Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers. Nat Biotechnol 2013; 31:325-30. [PMID: 23475072 DOI: 10.1038/nbt.2515] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 01/22/2013] [Indexed: 12/31/2022]
Abstract
Genes underlying mutant phenotypes can be isolated by combining marker discovery, genetic mapping and resequencing, but a more straightforward strategy for mapping mutations would be the direct comparison of mutant and wild-type genomes. Applying such an approach, however, is hampered by the need for reference sequences and by mutational loads that confound the unambiguous identification of causal mutations. Here we introduce NIKS (needle in the k-stack), a reference-free algorithm based on comparing k-mers in whole-genome sequencing data for precise discovery of homozygous mutations. We applied NIKS to eight mutants induced in nonreference rice cultivars and to two mutants of the nonmodel species Arabis alpina. In both species, comparing pooled F2 individuals selected for mutant phenotypes revealed small sets of mutations including the causal changes. Moreover, comparing M3 seedlings of two allelic mutants unambiguously identified the causal gene. Thus, for any species amenable to mutagenesis, NIKS enables forward genetics without requiring segregating populations, genetic maps and reference sequences.
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Galvão VC, Nordström KJV, Lanz C, Sulz P, Mathieu J, Posé D, Schmid M, Weigel D, Schneeberger K. Synteny-based mapping-by-sequencing enabled by targeted enrichment. Plant J 2012; 71:517-526. [PMID: 22409706 DOI: 10.1111/j.1365-313x.2012.04993.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Mapping-by-sequencing, as implemented in SHOREmap ('SHOREmapping'), is greatly accelerating the identification of causal mutations. The original SHOREmap approach based on resequencing of bulked segregants required a highly accurate and complete reference sequence. However, current whole-genome or transcriptome assemblies from next-generation sequencing data of non-model organisms do not produce chromosome-length scaffolds. We have therefore developed a method that exploits synteny with a related genome for genetic mapping. We first demonstrate how mapping-by-sequencing can be performed using a reduced number of markers, and how the associated decrease in the number of markers can be compensated for by enrichment of marker sequences. As proof of concept, we apply this method to Arabidopsis thaliana gene models ordered by synteny with the genome sequence of the distant relative Brassica rapa, whose genome has several large-scale rearrangements relative to A. thaliana. Our approach provides an alternative method for high-resolution genetic mapping in species that lack finished genome reference sequences or for which only RNA-seq assemblies are available. Finally, for improved identification of causal mutations by fine-mapping, we introduce a new likelihood ratio test statistic, transforming local allele frequency estimations into a confidence interval similar to conventional mapping intervals.
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Affiliation(s)
- Vinicius C Galvão
- Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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11
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Nordström KJV, Sällman Almén M, Edstam MM, Fredriksson R, Schiöth HB. Independent HHsearch, Needleman--Wunsch-based, and motif analyses reveal the overall hierarchy for most of the G protein-coupled receptor families. Mol Biol Evol 2011; 28:2471-80. [PMID: 21402729 DOI: 10.1093/molbev/msr061] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Several families of G protein-coupled receptors (GPCRs) show no significant sequence similarities to each other, and it has been debated which of them share a common origin. We developed and performed integrated and independent HHsearch, Needleman--Wunsch-based and motif analyses on more than 6,600 unique GPCRs from 12 species. Moreover, we mined the evolutionary important Trichoplax adhaerens, Nematostella vectensis, Thalassiosira pseudonana, and Strongylocentrotus purpuratus genomes, revealing remarkably rich vertebrate-like GPCR repertoires already in the early Metazoan species. We found strong evidence that the Adhesion and Frizzled families are children to the cyclic AMP (cAMP) family with HHsearch homology probabilities of 99.8% and 99.4%, respectively, also supported by the Needleman--Wunsch analysis and several motifs. We also found that the large Rhodopsin family is likely a child of the cAMP family with an HHsearch homology probability of 99.4% and conserved motifs. Therefore, we suggest that the Adhesion and Frizzled families originated from the cAMP family in an event close to that which gave rise to the Rhodopsin family. We also found convincing evidence that the Rhodopsin family is parent to the important sensory families; Taste 2 and Vomeronasal type 1 as well as the Nematode chemoreceptor families. The insect odorant, gustatory, and Trehalose receptors, frequently referred to as GPCRs, form a separate cluster without relationship to the other families, and we propose, based on these and others' results, that these families are ligand-gated ion channels rather than GPCRs. Overall, we suggest common descent of at least 97% of the GPCRs sequences found in humans.
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Affiliation(s)
- Karl J V Nordström
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Biomedical Center, Uppsala, Sweden
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Höglund PJ, Nordström KJV, Schiöth HB, Fredriksson R. The solute carrier families have a remarkably long evolutionary history with the majority of the human families present before divergence of Bilaterian species. Mol Biol Evol 2010; 28:1531-41. [PMID: 21186191 PMCID: PMC3058773 DOI: 10.1093/molbev/msq350] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [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: 01/11/2023] Open
Abstract
The Solute Carriers (SLCs) are membrane proteins that regulate transport of many types of substances over the cell membrane. The SLCs are found in at least 46 gene families in the human genome. Here, we performed the first evolutionary analysis of the entire SLC family based on whole genome sequences. We systematically mined and analyzed the genomes of 17 species to identify SLC genes. In all, we identified 4,813 SLC sequences in these genomes, and we delineated the evolutionary history of each of the subgroups. Moreover, we also identified ten new human sequences not previously classified as SLCs, which most likely belong to the SLC family. We found that 43 of the 46 SLC families found in Homo sapiens were also found in Caenorhabditis elegans, whereas 42 of them were also found in insects. Mammals have a higher number of SLC genes in most families, perhaps reflecting important roles for these in central nervous system functions. This study provides a systematic analysis of the evolutionary history of the SLC families in Eukaryotes showing that the SLC superfamily is ancient with multiple branches that were present before early divergence of Bilateria. The results provide foundation for overall classification of SLC genes and are valuable for annotation and prediction of substrates for the many SLCs that have not been tested in experimental transport assays.
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Affiliation(s)
- Pär J Höglund
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden
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13
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Abstract
The Adhesion family is unique among the GPCR (G protein-coupled receptor) families because of several features including long N-termini with multiple domains. The gene repertoire has recently been mined in great detail in several species including mouse, rat, dog, chicken and the early vertebrate Branchiostoma (Branchiostoma floridae) and one of the most primitive animals, the cniderian Nematostella (Nematostella vectensis). There is a one-to-one relationship of the rodent (mouse and rat) and human orthologues with the exception the EMR2 and EMR3 that do not seem to have orthologues in either rat or mouse. All 33 human Adhesion GPCR genes are present in the dog genome but the dog genome also contains 5 additional full-length Adhesion genes. The dog and human Adhesion orthologues have higher average protein sequence identity than the rodent (rat and mouse) and the human sequences. The Adhesion family is well-represented in chicken with 21 one-to-one orthologous with humans, while 12 human Adhesion GPCRs lack a chicken ortholog. Branchiostoma has rich repertoire of Adhesion GPCRs with at least 37 genes. Moreover, the Adhesion GPCRs in Branchiostoma have several novel domains their N-termini, like Somatomedin B, Kringle, Lectin C-type, SRCR, LDLa, Immunoglobulin I-set, CUB and TNFR. Nematostella has also Adhesion GPCRs that are show domain structure and sequence similarities in the transmembrane regions with different classes of mammalian GPCRs. The Nematostella genome has a unique set of Adhesion-like sequences lacking GPS domains. There is considerable evidence showing that the Adhesion family is ancestral to the peptide hormone binding Secretin family of GPCRs.
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Affiliation(s)
- Helgi B Schiöth
- Department of Neuroscience, Biomedical Center, Box 593, 75 124 Uppsala, Sweden.
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Nordström KJV, Mirza MAI, Almén MS, Gloriam DE, Fredriksson R, Schiöth HB. Critical evaluation of the FANTOM3 non-coding RNA transcripts. Genomics 2009; 94:169-76. [PMID: 19505569 DOI: 10.1016/j.ygeno.2009.05.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 05/25/2009] [Accepted: 05/26/2009] [Indexed: 01/15/2023]
Abstract
We studied the genomic positions of 38,129 putative ncRNAs from the RIKEN dataset in relation to protein-coding genes. We found that the dataset has 41% sense, 6% antisense, 24% intronic and 29% intergenic transcripts. Interestingly, 17,678 (47%) of the FANTOM3 transcripts were found to potentially be internally primed from longer transcripts. The highest fraction of these transcripts was found among the intronic transcripts and as many as 77% or 6929 intronic transcripts were both internally primed and unspliced. We defined a filtered subset of 8535 transcripts that did not overlap with protein-coding genes, did not contain ORFs longer than 100 residues and were not internally primed. This dataset contains 53% of the FANTOM3 transcripts associated to known ncRNA in RNAdb and expands previous similar efforts with 6523 novel transcripts. This bioinformatic filtering of the FANTOM3 non-coding dataset has generated a lead dataset of transcripts without signs of being artefacts, providing a suitable dataset for investigation with hybridization-based techniques.
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Fredriksson R, Nordström KJV, Stephansson O, Hägglund MGA, Schiöth HB. The solute carrier (SLC) complement of the human genome: phylogenetic classification reveals four major families. FEBS Lett 2008; 582:3811-6. [PMID: 18948099 DOI: 10.1016/j.febslet.2008.10.016] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 10/03/2008] [Accepted: 10/10/2008] [Indexed: 10/21/2022]
Abstract
Solute carriers (SLCs) is the largest group of transporters, embracing transporters for inorganic ions, amino acids, neurotransmitters, sugars, purines and fatty acids among other substrates. We mined the finished assembly of the human genome using Hidden Markov Models (HMMs) obtaining a total of 384 unique SLC sequences. Detailed clustering and phylogenetic analysis of the entire SLC family showed that 15 of the families place into four large phylogenetic clusters with the largest containing eight SLC families, suggesting that many of the distinct families of SLCs have a common evolutionary origin. This study represents the first overall genomic roadmap of the SLCs providing large sequence sets and clarifies the phylogenetic relationships among the families of the second largest group of membrane proteins.
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Affiliation(s)
- Robert Fredriksson
- Department of Neuroscience, Unit of Functional Pharmacology, Uppsala University, BMC, Uppsala SE 75124, Sweden.
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Nordström KJV, Lagerström MC, Wallér LMJ, Fredriksson R, Schiöth HB. The Secretin GPCRs descended from the family of Adhesion GPCRs. Mol Biol Evol 2008; 26:71-84. [PMID: 18845549 DOI: 10.1093/molbev/msn228] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Adhesion G-protein-coupled receptors (GPCRs) are the most complex gene family among GPCRs with large genomic size, multiple introns, and a fascinating flora of functional domains, though the evolutionary origin of this family has been obscure. Here we studied the evolution of all class B (7tm2)-related genes, including the Adhesion, Secretin, and Methuselah families of GPCRs with a focus on nine genomes. We found that the cnidarian genome of Nematostella vectensis has a remarkably rich set of Adhesion GPCRs with a broad repertoire of N-terminal domains although this genome did not have any Secretin GPCRs. Moreover, the single-celled and colony-forming eukaryotes Monosiga brevicollis and Dictyostelium discoideum contain Adhesion-like GPCRs although these genomes do not have any Secretin GPCRs suggesting that the Adhesion types of GPCRs are the most ancient among class B GPCRs. Phylogenetic analysis found Adhesion group V (that contains GPR133 and GPR144) to be the closest relative to the Secretin family in the Adhesion family. Moreover, Adhesion group V sequences in N. vectensis share the same splice site setup as the Secretin GPCRs. Additionally, one of the most conserved motifs in the entire Secretin family is only found in group V of the Adhesion family. We suggest therefore that the Secretin family of GPCRs could have descended from group V Adhesion GPCRs. We found a set of unique Adhesion-like GPCRs in N. vectensis that have long N-termini containing one Somatomedin B domain each, which is a domain configuration similar to that of a set of Adhesion-like GPCRs found in Branchiostoma floridae. These sequences show slight similarities to Methuselah sequences found in insects. The extended class B GPCRs have a very complex evolutionary history with several species-specific expansions, and we identified at least 31 unique N-terminal domains originating from other protein classes. The overall N-terminal domain structure, however, concurs with the phylogenetic analysis of the transmembrane domains, thus enabling us to track the origin of most of the subgroups.
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Affiliation(s)
- Karl J V Nordström
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden
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Nordström KJV, Fredriksson R, Schiöth HB. The amphioxus (Branchiostoma floridae) genome contains a highly diversified set of G protein-coupled receptors. BMC Evol Biol 2008; 8:9. [PMID: 18199322 PMCID: PMC2246102 DOI: 10.1186/1471-2148-8-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [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] [Received: 08/15/2007] [Accepted: 01/16/2008] [Indexed: 11/24/2022] Open
Abstract
Background G protein-coupled receptors (GPCRs) are one of the largest families of genes in mammals. Branchiostoma floridae (amphioxus) is one of the species most closely related species to vertebrates. Results Mining and phylogenetic analysis of the amphioxus genome showed the presence of at least 664 distinct GPCRs distributed among all the main families of GPCRs; Glutamate (18), Rhodopsin (570), Adhesion (37), Frizzled (6) and Secretin (16). Surprisingly, the Adhesion GPCR repertoire in amphioxus includes receptors with many new domains not previously observed in this family. We found many Rhodopsin GPCRs from all main groups including many amine and peptide binding receptors and several previously uncharacterized expansions were also identified. This genome has however no genes coding for bitter taste receptors (TAS2), the sweet and umami (TAS1), pheromone (VR1 or VR2) or mammalian olfactory receptors. Conclusion The amphioxus genome is remarkably rich in various GPCR subtypes while the main GPCR groups known to sense exogenous substances (such as Taste 2, mammalian olfactory, nematode chemosensory, gustatory, vomeronasal and odorant receptors) in other bilateral species are absent.
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Affiliation(s)
- Karl J V Nordström
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24, Uppsala, Sweden.
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Abstract
The purpose of this article was to review recent progress in mining the gene repertoire and expressed sequence tags (ESTs) for the super-family of G protein-coupled receptors (GPCRs) in the form of a proceeding from the Nordic GPCR meeting held at the Nobel Forum, Karolinska Institute in August 2006. We update and give an overview of the expansion of the main families of GPCRs; Glutamate, Rhodopsin, Adhesion, Frizzled and Secretin (GRAFS) in perspective of fully sequenced genomes. We look into the most recent findings including the work that has been carried out on the spotted green puffer fish (Tetraodon nigroviridis), mouse (Mus musculus), chicken (Gallus gallus), slime mold (Dictyostelium discoideum) and the plant pathogenic fungus Magnaporthe grisea. We use examples from our recent work on chicken GPCRs to highlight the importance of detailed assembly and curation of sequences and how that can affect percentage similarity and phylogeny. ESTs can give valuable information about expression patterns. GPCRs have comparatively low numbers of EST suggesting that GPCRs are in generally expressed in lower amount than other genes. We discuss similarities in the evolution of the trace amine associated receptors with other sensory receptors.
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Affiliation(s)
- H B Schiöth
- Department of Neuroscience, Uppsala University, Uppsala, Sweden.
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Nordström KJV, Mirza MAI, Larsson TP, Gloriam DEI, Fredriksson R, Schiöth HB. Comprehensive comparisons of the current human, mouse, and rat RefSeq, Ensembl, EST, and FANTOM3 datasets: Identification of new human genes with specific tissue expression profile. Biochem Biophys Res Commun 2006; 348:1063-74. [PMID: 16904064 DOI: 10.1016/j.bbrc.2006.07.153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Accepted: 07/25/2006] [Indexed: 10/24/2022]
Abstract
Our understanding of functional genetic elements in the genomes is continuously growing and new entries are entered in various databases on a regular basis. We have here merged the genetic elements in RefSeq, Ensembl, FANTOM3, HINV, and NCBI:s ESTdb using the genome assemblies in order to achieve a comprehensive picture of the current status of the identity and gene number in human, mouse, and rat. The number of human protein coding genes has not increased (25,043) while the increased sequencing of mouse transcripts has provided the considerably higher number of protein coding genes (31,578) in mouse. The results indicate large discrepancies between the datasets, as considerable numbers of unique transcripts can be found in each dataset. Despite the high number of ncRNA (38,129 in mouse) there are also almost 20,000 EST clusters in both mouse and humans with more than one EST that do not overlap any transcript suggesting that several new genetic elements are still to be found. We also demonstrated presence of new genes by identifying new human ones that have specific tissue profiles, using RT-PCR on rat tissues.
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Affiliation(s)
- Karl J V Nordström
- Department of Neuroscience, Uppsala University, BMC Box 593, 751 24 Uppsala, Sweden
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