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39 results on '"Gregor Mendel Institute of Molecular Plant Biology (GMI)"'

1. Genome-wide binding-site analysis of REVOLUTA reveals a link between leaf patterning and light-mediated growth responses

Author

Brandt, Ronny, Salla-Martret, Merce, Bou-Torrent, Jordi, Musielak, Thomas, Stahl, Mark, Lanz, Christa, Ott, Felix, Schmid, Markus, Greb, Thomas, Schwarz, Martina, Choi, Sang-Bong, Barton, M. Kathryn, Reinhart, Brenda J., Liu, Tie, Quint, Marcel, Palauqui, Jean-Christophe, Martinez-Garcia, Jaime F., Wenkel, Stephan, National Science Foundation (US), Generalitat de Catalunya, Ministerio de Ciencia e Innovación (España), German Research Foundation, Robert Bosch Foundation, Federal Ministry of Food and Agriculture (Germany), European Commission, Zentrum für Molekularbiologie der Pflanzen (ZMBP), Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Department of Molecular Biology [Tübingen], Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Sch Biotechnol & Environm Engn, Myongji Univ, Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science [Washington], Dept Mol Signal Proc, D-06120 Halle, Leibniz Institute of Plant Biochemistry (IPB), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Carnegie Institution for Science, National Science Foundation (NSF) [0929413], Generalitat de Catalunya (Xarba) [2009-SGR697], MICINN - FEDER funds [BIO2005-00154, CSD2007-00036, BIO2008-00169], Deutsche Forschungsgemeinschaft (DFG) [WE4281/6-1], European Union [256502], Ministry for Agriculture (Bundesanstalt fur Landwirtschaft und Ernahrung) [CHN 13-22/12-13], Eberhard Karls Universität Tübingen, Department of Plant Biology [Carnegie Institution], Zentrum für Molekularbiologie der Pflanzen ( ZMBP ), Dept Mol Biol, Gregor Mendel Institute of Molecular Plant Biology ( GMI ), Austrian Academy of Sciences ( OeAW ), Leibniz Institute of Plant Biochemistry, Institut Jean-Pierre Bourgin ( IJPB ), and Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Arabidopsis thaliana, PLANT DEVELOPMENT, fungi, HD-ZIPIII, SHADE-AVOIDANCE RESPONSES, ARABIDOPSIS, GENE, HD-ZIPII, CELL FATE, TRANSCRIPTION, auxin, AUXIN BIOSYNTHESIS, REGULATOR, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, shade avoidance, ZIP, leaf development, POLARITY
Abstract

Unlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) transcription factors are involved in embryo, shoot and root patterning. During vegetative growth HD-ZIPIII proteins control several polarity set-up processes such as in leaves and the vascular system. We have identified several direct target genes of the HD-ZIPIII transcription factor REVOLUTA (REV) using a chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) approach. This analysis revealed that REV acts upstream of auxin biosynthesis and affects directly the expression of several class II HD-ZIP transcription factors that have been shown to act in the shade-avoidance response pathway. We show that, as well as involvement in basic patterning, HD-ZIPIII transcription factors have a critical role in the control of the elongation growth that is induced when plants experience shade. Leaf polarity is established by the opposed actions of HD-ZIPIII and KANADI transcription factors. Finally, our study reveals that the module that consists of HD-ZIPIII/KANADI transcription factors controls shade growth antagonistically and that this antagonism is manifested in the opposed regulation of shared target genes., The Barton lab receives funding from the Carnegie Institution for Science and the National Science Foundation (NSF2010, grant #0929413). Research in the JFM-G laboratory is supported by grants from the Generalitat de Catalunya (Xarba, 2009-SGR697) and MICINN – FEDER funds (BIO2005-00154, CSD2007-00036, BIO2008-00169). Research in the SW laboratory is made possible by funding from the Deutsche Forschungsgemeinschaft (DFG, WE4281/6-1), the European Union (FP7 No. 256502), the Robert Bosch Foundation and the Ministry for Agriculture (Bundesanstalt für Landwirtschaft und Ernährung; CHN13-22/12-13) to SW.

Published
2012

2. Chaperone-like protein DAY plays critical roles in photomorphogenesis

Author

Sung Hee Lee, Hee-Kyung Ahn, Tak Lee, Insuk Lee, Hyun Sook Pai, Ilyeong Choi, Dong Hye Seo, Ji Woo Kim, Ho Seok Lee, Huikyong Cho, Jae Hee Kim, Julian Bünting, Young Eun Jeon, Youssef Belkhadir, D. Lee, Tae Wuk Kim, Jung Min Lee, Man Ho Oh, Ahn, Hee-Kyung [0000-0002-8884-0156], Lee, Tak [0000-0001-7008-7605], Lee, Du-Hwa [0000-0003-4106-7730], Lee, Insuk [0000-0003-3146-6180], Belkhadir, Youssef [0000-0001-7149-7139], Pai, Hyun-Sook [0000-0003-1345-5840], Apollo - University of Cambridge Repository, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Yonsei University Seoul, Korea, University of East Anglia [Norwich] (UEA), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), College of Life Sciences and Biotechnology, Korea University, Chungnam National University (CNU), Hanyang University, Vienna Biocenter - VBC [Austria], and Yonsei University

Subjects
0106 biological sciences, 0301 basic medicine, Chlorophyll, Chloroplasts, Light, [SDV]Life Sciences [q-bio], Arabidopsis, General Physics and Astronomy, 631/449/2653/1359, 01 natural sciences, chemistry.chemical_compound, 38/1, Gene Expression Regulation, Plant, Morphogenesis, Brassinosteroid, RNA-Seq, 14/19, 13/89, Multidisciplinary, biology, Chemistry, article, Plant morphogenesis, Plant physiology, food and beverages, Plants, Genetically Modified, Recombinant Proteins, Cell biology, Chloroplast, Transmembrane domain, Gene Knockdown Techniques, Photomorphogenesis, 38/39, Microtubule-Associated Proteins, Signal Transduction, Science, 38/90, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Brassinosteroids, Etiolation, Light responses, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Endomembrane system, 14/35, 631/449/2686, Arabidopsis Proteins, fungi, Membrane Proteins, General Chemistry, HSP40 Heat-Shock Proteins, 030104 developmental biology, Seedlings, Chaperone (protein), Mutation, 14/63, biology.protein, Protein Kinases, Biogenesis, 010606 plant biology & botany
Abstract

Photomorphogenesis, light-mediated development, is an essential feature of all terrestrial plants. While chloroplast development and brassinosteroid (BR) signaling are known players in photomorphogenesis, proteins that regulate both pathways have yet to be identified. Here we report that DE-ETIOLATION IN THE DARK AND YELLOWING IN THE LIGHT (DAY), a membrane protein containing DnaJ-like domain, plays a dual-role in photomorphogenesis by stabilizing the BR receptor, BRI1, as well as a key enzyme in chlorophyll biosynthesis, POR. DAY localizes to both the endomembrane and chloroplasts via its first transmembrane domain and chloroplast transit peptide, respectively, and interacts with BRI1 and POR in their respective subcellular compartments. Using genetic analysis, we show that DAY acts independently on BR signaling and chlorophyll biogenesis. Collectively, this work uncovers DAY as a factor that simultaneously regulates BR signaling and chloroplast development, revealing a key regulator of photomorphogenesis that acts across cell compartments., Chloroplast development and brassinosteroid (BR) signaling both regulate plant photomorphogenesis. Here the authors show that DAY, a DnaJ-like domain-containing membrane protein, regulates both processes by binding and stabilizing both BRI1, the BR receptor, and POR, a key enzyme in chlorophyll biosynthesis.

Published
2021
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3. Role of Polycomb in the control of transposable elements

Author

Sandra Duharcourt, Angélique Déléris, Frédéric Berger, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Institut Jacques Monod (IJM (UMR_7592)), Université de Paris (UP)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), This work was supported by Centre National de la Recherche Scientifique, the LABEX Who Am I? (ANR-11-LABX-0071, ANR-11-IDEX-0005-02), the Agence Nationale de la Recherche (ANR-18-CE12-0005-04, ANR-19-CE12-0015-01 to S.D., ANR-19-CE12-0033-01 to A.D.), and theAustrian Science Fund (FWF grants P30802, P32054, and TAI304 to F.B.), ANR-11-LABX-0071,WHO AM I,Determinants de l'Identité : de la molécule à l'individu(2011), ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011), ANR-18-CE12-0005,LaMarque,Transitions évolutives dans la reconnaissance du 'soi' génomique: petits ARN, facteurs spécifiques de séquence et méthylation de l'ADN(2018), ANR-19-CE12-0015,POLYCHROME,Complexe Polycomb chez la paramécie: interaction avec la machinerie des petits ARN et spécificité de substrats(2019), and ANR-19-CE12-0033,COMPTES,COopération, COmpensation, COmpétition: interactions complexes entre Méthylation de l'ADN et Polycomb dans le contrôle des Eléments Transposables d'ArabidopsiS(2019)

Subjects
Transposable element, Heterochromatin, Mutant, Polycomb-Group Proteins, macromolecular substances, Histones, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Animals, Humans, Gene, 030304 developmental biology, 0303 health sciences, biology, Polycomb Repressive Complex 2, DNA Methylation, Histone, chemistry, Evolutionary biology, DNA methylation, DNA Transposable Elements, biology.protein, PRC2, 030217 neurology & neurosurgery, DNA
Abstract

It is generally considered that Polycomb Repressive Complex (PRC)2 deposits the histone mark H3K27me3 on silent protein-coding genes, while transposable elements are repressed by DNA and/or H3K9 methylation. Yet, there is increasing evidence that PRC2 also targets and even silences transposable elements in representatives of several distantly related eukaryotic lineages. In plants and animals, H3K27me3 is present on transposable elements in mutants and specific cell types devoid of DNA methylation. In this Opinion, we summarize the experimental evidence for this phenomenon across the eukaryotic kingdom, and discuss its functional and evolutionary significance. We hypothesize that an ancestral role of Polycomb group (PcG) proteins was to silence transposable elements.

Published
2021

4. Loss of two families of SPX domain-containing proteins required for vacuolar polyphosphate accumulation coincides with the transition to phosphate storage in green plants

Author

Liam Dolan, Benoît Menand, Houqing Zeng, Hongyu Zhao, Long Wang, Lei Xu, Xianqing Jia, Keke Yi, Yuxin Zhang, Yiyong Zhu, Key Laboratory of Plant Nutrition and Fertilizers, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences (CAAS), Nanjing Agricultural University (NAU), Luminy Génétique et Biophysique des Plantes (LGBP), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), College of Life and Environmental Sciences, Hangzhou Normal University, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China, European Project: 787613,DENOVO-P, Nanjing Agricultural University, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0301 basic medicine, SPX-VTC, [SDV]Life Sciences [q-bio], SPX-SLC, plant evolution, chemistry.chemical_element, Chlamydomonas reinhardtii, Plant Science, Vacuole, Viridiplantae, 01 natural sciences, 03 medical and health sciences, Polyphosphates, Homeostasis, Molecular Biology, Phylogeny, Plant Proteins, biology, Permease, Phosphorus, Chlamydomonas, polyphosphate, biology.organism_classification, Solute carrier family, vacuolar phosphate, 030104 developmental biology, Biochemistry, chemistry, Chaperone (protein), Vacuoles, biology.protein, 010606 plant biology & botany, Molecular Chaperones
Abstract

International audience; Phosphorus is an essential nutrient for plants. It is stored as inorganic phosphate (Pi) in the vacuoles of land plants but as inorganic polyphosphate (polyP) in chlorophyte algae. Although it is recognized that the SPXMajor Facilitator Superfamily (MFS) and VPE proteins are responsible for Pi influx and efflux, respectively, across the tonoplast in land plants, the mechanisms that underlie polyP homeostasis and the transition of phosphorus storage forms during the evolution of green plants remain unclear. In this study, we showed that CrPTC1, encoding a protein with both SPX and SLC (permease solute carrier 13) domains for Pi transport, and CrVTC4, encoding a protein with both SPX and vacuolar transporter chaperone (VTC) domains for polyP synthesis, are required for vacuolar polyP accumulation in the chlorophyte Chlamydomonas reinhardtii. Phylogenetic analysis showed that the SPX-SLC, SPX-VTC, and SPX-MFS proteins were present in the common ancestor of green plants (Viridiplantae). The SPX-SLC and SPX-VTC proteins are conserved among species that store phosphorus as vacuolar polyP and absent from genomes of plants that store phosphorus as vacuolar Pi. By contrast, SPX-MFS genes are present in the genomes of streptophytes that store phosphorus as Pi in the vacuoles. These results suggest that loss of SPX-SLC and SPX-VTC genes and functional conservation of SPX-MFS proteins during the evolution of streptophytes accompanied the change from ancestral polyP storage to Pi storage.

Published
2020

5. DEK influences the trade-off between growth and 1 arrest via H2A.Z-nucleosomes in Arabidopsis

Author

Brestovitsky, Anna, Ezer, Daphne, Waidmann, Sascha, Maslen, Sarah, Balcerowicz, Martin, Cortijo, Sandra, Charoensawan, Varodom, Rhodes, Daniela, Jonak, Claudia, Wigge, Philip, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), University of Natural Resources and Life Sciences (BOKU), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Nanyang Technological University [Singapour], Sainsbury Laboratory Cambridge, University of Natural Resources and Applied Life Sciences (BOKU), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
stomatognathic diseases, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics
Abstract

The decision of whether to grow and proliferate or to restrict growth and develop resilience to stress is a key biological trade-off. In plants, constitutive growth results in increased sensitivity to environmental stress1,2. The underlying mechanisms controlling this decision are however not well understood. We used temperature as a cue to discover regulators of this process in plants, as it both enhances growth and development rates within a specific range and is also a stress at extremes. We found that the conserved chromatin-associated protein DEK plays a central role in balancing the response between growth and arrest in Arabidopsis, and it does this via H2A.Z-nucleosomes. DEK target genes show two distinct categories of chromatin architecture based on the distribution of H2A.Z in +1 nucleosome and gene body, and these predict induction or repression by DEK. We show that these chromatin signatures of DEK target genes are conserved in human cells, suggesting that DEK may act through an evolutionarily conserved mechanism to control the balance between growth and arrest in plants and animals.

Published
2020

6. Arabidopsis proteins with a transposon-related domain act in gene silencing

Author

Yoko, Ikeda, Thierry, Pélissier, Pierre, Bourguet, Claude, Becker, Marie-Noëlle, Pouch-Pélissier, Romain, Pogorelcnik, Magdalena, Weingartner, Detlef, Weigel, Jean-Marc, Deragon, Olivier, Mathieu, Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Université de Perpignan Via Domitia (UPVD), Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Retroelements, Arabidopsis Proteins, [SDV]Life Sciences [q-bio], Science, Centromere, Arabidopsis, Nuclear Proteins, food and beverages, DNA Methylation, Article, Evolution, Molecular, Protein Domains, Heterochromatin, DNA Transposable Elements, Gene Silencing, RNA, Small Interfering, ComputingMilieux_MISCELLANEOUS
Abstract

Transposable elements (TEs) are prevalent in most eukaryotes, and host genomes have devised silencing strategies to rein in TE activity. One of these, transcriptional silencing, is generally associated with DNA methylation and short interfering RNAs. Here we show that the Arabidopsis genes MAIL1 and MAIN define an alternative silencing pathway independent of DNA methylation and short interfering RNAs. Mutants for MAIL1 or MAIN exhibit release of silencing and appear to show impaired condensation of pericentromeric heterochromatin. Phylogenetic analysis suggests not only that MAIL1 and MAIN encode a retrotransposon-related plant mobile domain, but also that host plant mobile domains were captured by DNA transposons during plant evolution. Our results reveal a role for Arabidopsis proteins with a transposon-related domain in gene silencing., Host genomes have evolved multiple silencing mechanisms to repress transposable element activity. Here Ikeda et al. show that the Arabidopsis MAIL1 and MAIN genes encode a retrotransposon-related plant mobile domain and define an alternative silencing pathway largely independent of DNA methylation and siRNAs.

Published
2017

7. Molecular characterization of Chlamydomonas reinhardtii telomeres and telomerase mutants

Author

Eberhard, Stephan, Valuchova, Sona, Ravat, Julie, Fulneček, Jaroslav, Jolivet, Pascale, Bujaldon, Sandrine, Lemaire, Stéphane, Wollman, Francis-André, Teixeira, Maria Teresa, Riha, Karel, Xu, Zhou, Physiologie membranaire et moléculaire du chloroplaste (PMMC), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes (LBMCE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris Seine (IBPS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Base Sequence, [SDV]Life Sciences [q-bio], Genetic Variation, Telomere Homeostasis, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, macromolecular substances, Telomere, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Amino Acid Sequence, Telomerase, Research Articles, Chlamydomonas reinhardtii, Polymorphism, Restriction Fragment Length, Telomere Shortening, Research Article, Repetitive Sequences, Nucleic Acid
Abstract

This study characterizes the sequence, end structure, and length distribution of Chlamydomonas reinhardtii telomeres and shows that telomerase mutants are defective in telomere maintenance., Telomeres are repeated sequences found at the end of the linear chromosomes of most eukaryotes and are required for chromosome integrity. Expression of the reverse-transcriptase telomerase allows for extension of telomeric repeats to counteract natural telomere shortening. Although Chlamydomonas reinhardtii, a photosynthetic unicellular green alga, is widely used as a model organism in photosynthesis and flagella research, and for biotechnological applications, the biology of its telomeres has not been investigated in depth. Here, we show that the C. reinhardtii (TTTTAGGG)n telomeric repeats are mostly nondegenerate and that the telomeres form a protective structure, with a subset ending with a 3′ overhang and another subset presenting a blunt end. Although telomere size and length distributions are stable under various standard growth conditions, they vary substantially between 12 genetically close reference strains. Finally, we identify CrTERT, the gene encoding the catalytic subunit of telomerase and show that telomeres shorten progressively in mutants of this gene. Telomerase mutants eventually enter replicative senescence, demonstrating that telomerase is required for long-term maintenance of telomeres in C. reinhardtii.

Published
2019

8. Ancient hybridization and strong adaptation to viruses across African vervet monkey populations

Author

Svardal, Hannes, Jasinska, Anna, Apetrei, Cristian, Coppola, Giovanni, Huang, Yu, Schmitt, Christopher, Jacquelin, Béatrice, Ramensky, Vasily, Müller-Trutwin, Michaela, Antonio, Martin, Weinstock, George, Grobler, J. Paul, Dewar, Ken, Wilson, Richard, Turner, Trudy, Warren, Wesley, Freimer, Nelson, Nordborg, Magnus, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), University of California [Los Angeles] (UCLA), University of California (UC), Polish Academy of Sciences (PAN), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Shanghai Institute of Materia Medica, Chinese Academy of Sciences [Changchun Branch] (CAS), Boston University [Boston] (BU), HIV, Inflammation et persistance - HIV, Inflammation and Persistence, Institut Pasteur [Paris] (IP), Moscow Institute of Physics and Technology [Moscow] (MIPT), Medical Research Council Unit The Gambia (MRC), The Jackson Laboratory [Bar Harbor] (JAX), University of the Free State [South Africa] (UFS), McGill University = Université McGill [Montréal, Canada], University of Wisconsin - Milwaukee, The McDonnell Genome Institute (MGI), Washington University in Saint Louis (WUSTL), H.S. has been supported by a travel grant from the Austrian Ministry of Science and Research. C.A. is supported by RO1 AI119346 from the National Institute of Allergy and Infectious Diseases (NIAID). We acknowledge the support of the National Institute of Neurological Disorders and Stroke (NINDS) Informatics Center for Neurogenetics and Neurogenomics (P30 NS062691). We would like to thank F. Gao for assistance with microarray data analysis., Samples were collected through the UCLA Systems Biology Sample Repository funded by US National Institutes of Health grants R01RR016300 and R01OD010980 to N.F. For permits allowing us to collect samples, we thank the Gambia Department of Parks & Wildlife Management, the Botswana Ministry of Environment & Wildlife and Tourism, the Ghana Wildlife Division, Forestry Commission, the Zambia Wildlife Authority, the Ethiopian Wildlife Conservation Authority, the Ministry of Forestry & the Environment, Department of Environmental Affairs, South Africa, the Department of Economic Development and Environmental Affairs, Eastern Cape, the Department of Tourism, Environmental and Economic Affairs, Free State, Ezemvelo KZN Wildlife, KwaZulu-Natal, and the Department of Economic Development, Environment and Tourism, Limpopo. We also thank G. Redmond and the St. Kitts Biomedical Research Foundation for facilitating sample collection in St. Kitts and Nevis. We thank J. Brenchley, K. Reimann (R24OD010976), and J. Baulu and the Barbados Primate Research Center and Wildlife Reserve for providing samples of Tanzanian origin and Barbadian vervets. For help with sample collection and processing, we thank J. Danzy-Cramer, Y. Jung, O. Morton and J. Freimer. We thank J. Kamm for discussion, Ü. Seren, J. Wasserscheid and N. Juretic for IT support, and R. Halai for help with figure design, University of California, HIV, Inflammation et persistance, Institut Pasteur [Paris], and University of the Free State [South Africa]

Subjects
CD4-Positive T-Lymphocytes, animal diseases, [SDV]Life Sciences [q-bio], Simian Acquired Immunodeficiency Syndrome, medicine.disease_cause, Medical and Health Sciences, 0302 clinical medicine, Reticulate, Chlorocebus aethiops, Gene Regulatory Networks, Vervet monkey, Phylogeny, Genetics, 0303 health sciences, [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Simian immunodeficiency virus, Biological Sciences, Phenotype, Host-Pathogen Interactions, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Biotechnology, Physiological, Biology, 03 medical and health sciences, Acquired immunodeficiency syndrome (AIDS), Genetic, Species Specificity, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], parasitic diseases, medicine, Animals, Adaptation, Gene, Hybridization, 030304 developmental biology, Gene Expression Profiling, Human Genome, Genetic Variation, biology.organism_classification, medicine.disease, Macaca mulatta, Gene Ontology, Good Health and Well Being, Africa, African Green Monkey, 030217 neurology & neurosurgery, Developmental Biology
Abstract

Vervet monkeys (genusChlorocebus, also known as African green monkeys), are highly abundant in savannahs and riverine forests throughout sub-Saharan Africa. They are amongst the most widely distributed nonhuman primates, show considerable phenotypic diversity, and have long been an important biomedical model for a variety of human diseases and in vaccine research. They are particularly interesting for HIV/AIDS research as they are the most abundant natural hosts of simian immunodeficiency virus (SIV), a close relative of HIV. Here we present the first genome-wide survey of polymorphism in vervets, using sequencing data from 163 individuals sampled from across Africa and the Caribbean islands where vervets were introduced during the colonial era. We find high diversity, within and between taxa, and clear evidence that taxonomic divergence was reticulate rather than following a simple branching pattern. A scan for diversifying selection across vervet taxa yields gene enrichments much stronger than in similar studies on humans. In particular, we report strong and highly polygenic selection signals affecting viral processes --- in line with recent evidence that proposes a driving role for viruses in protein evolution in mammals. Furthermore, selection scores are highly elevated in genes whose human orthologs interact with HIV, and in genes that show a response to experimental SIV infection in vervet monkeys but not in rhesus macaques, suggesting that part of the signal reflects taxon-specific adaptation to SIV. Intriguingly, rather than affecting genes with antiviral and inflammatory-related functions, selection in vervets appears to have primarily targeted genes involved in the transcriptional regulation of viruses, and in particular those that are harmful only under immunodeficiency, suggesting adaptation to living with SIV rather than defense against infection.

Published
2019

9. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Author

Sieberts, Solveig K., Zhu, Fan, García-García, Javier, Stahl, Eli, Pratap, Abhishek, Pandey, Gaurav, Pappas, Dimitrios, Aguilar, Daniel, Anton, Bernat, Bonet, Jaume, Eksi, Ridvan, Fornés, Oriol, Guney, Emre, Li, Hongdong, Marín, Manuel Alejandro, Panwar, Bharat, Planas-Iglesias, Joan, Poglayen, Daniel, Cui, Jing, Falcao, Andre O., Suver, Christine, Hoff, Bruce, Balagurusamy, Venkat S. K., Dillenberger, Donna, Neto, Elias Chaibub, Norman, Thea, Aittokallio, Tero, Ammad-ud-din, Muhammad, Azencott, Chloe-Agathe, Bellón, Víctor, Boeva, Valentina, Bunte, Kerstin, Chheda, Himanshu, Cheng, Lu, Corander, Jukka, Dumontier, Michel, Goldenberg, Anna, Gopalacharyulu, Peddinti, Hajiloo, Mohsen, Hidru, Daniel, Jaiswal, Alok, Kaski, Samuel, Khalfaoui, Beyrem, Khan, Suleiman Ali, Kramer, Eric R., Marttinen, Pekka, Mezlini, Aziz M., Molparia, Bhuvan, Pirinen, Matti, Saarela, Janna, Samwald, Matthias, Stoven, Véronique, Tang, Hao, Tang, Jing, Torkamani, Ali, Vert, Jean-Phillipe, Wang, Bo, Wang, Tao, Wennerberg, Krister, Wineinger, Nathan E., Xiao, Guanghua, Xie, Yang, Yeung, Rae, Zhan, Xiaowei, Zhao, Cheng, Calaza, Manuel, Elmarakeby, Haitham, Heath, Lenwood S., Long, Quan, Moore, Jonathan D., Opiyo, Stephen Obol, Savage, Richard S., Zhu, Jun, Greenberg, Jeff, Kremer, Joel, Michaud, Kaleb, Barton, Anne, Coenen, Marieke, Mariette, Xavier, Miceli, Corinne, Shadick, Nancy, Weinblatt, Michael, de Vries, Niek, Tak, Paul P., Gerlag, Danielle, Huizinga, Tom W. J., Kurreeman, Fina, Allaart, Cornelia F., Louis Bridges Jr., S., Criswell, Lindsey, Moreland, Larry, Klareskog, Lars, Saevarsdottir, Saedis, Padyukov, Leonid, Gregersen, Peter K., Friend, Stephen, Plenge, Robert, Stolovitzky, Gustavo, Oliva, Baldo, Guan, Yuanfang, Mangravite, Lara M., Bridges, S. Louis, Intelligent Systems, Institute for Molecular Medicine Finland, Department of Mathematics and Statistics, Helsinki Institute for Information Technology, Jukka Corander / Principal Investigator, Department of Computer Science, Janna Saarela / Principal Investigator, Krister Wennerberg / Principal Investigator, Biostatistics Helsinki, Statistical and population genetics, AII - Amsterdam institute for Infection and Immunity, Clinical Immunology and Rheumatology, Zhejiang University, Universidad del Pais Vasco / Euskal Herriko Unibertsitatea [Espagne] (UPV/EHU), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), DYNBIO LEGOS, Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Institut d'Ecologia Aquàtica, Universitat de Girona (UdG), Department of Medical Genetics, Faculty of Medicine-Child and Family Research Institute-Centre for Molecular Medicine and Therapeutics-University of British Columbia (UBC), China Agricultural University (CAU), Computational Intelligence Research Group (CA3), Centre of Technology and Systems (CTS), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Bioinformatique (CBIO), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Hefei University of Technology (HFUT), Stanford Center for BioMedical Informatics Research (BMIR), Stanford University, Service de génétique [Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Technical Research Centre of Finland, VTT Technical Research Centre of Finland (VTT), U.S. Food and Drug Administration (FDA), Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Profium Oy [Helsinki], Chinese Academy of Agricultural Sciences (CAAS), Business School [Hohai University], Hohai University, Institute of Industrial Economics [Hohai University], State Key Laboratory of Medical Genetics of China, Hunan Medical College, State Key Laboratory of Advanced Special Steel, Shanghai University, Quantitative Biomedical Research Center (QBRC), University of Texas Southwestern Medical Center [Dallas], Harold C. Simmons Comprehensive Cancer Center [Dallas, TX, États-Unis], Laboratoire de recherche en Hydrodynamique, Énergétique et Environnement Atmosphérique (LHEEA), École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), China National Research Center of Intelligent Equipment for Agriculture [Beijing] (NRCIEA), Centro Nacional de Análisi Genómico (CNAG), Centro Nacional de Análisis Genómico, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Department of Mechanical and Aerospace Engineering [Univ California Davis] (MAE - UC Davis), University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), Tongji University, Laboratory for Measles and Rubella, Laboratoire National de Santé [Luxembourg] (LNS), Department of Human Genetics, Radboud University Medical Center [Nijmegen], INSERM U1012, AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), School of biosciences and biotechnology, University of Camerino, Università degli Studi di Camerino = University of Camerino (UNICAM), Division of Rheumatology, Immunology and Allergy and Partners Asthma Center, Brigham and Women's Hospital [Boston], Department of Health Education and Promotion, Maastricht University [Maastricht], University of Amsterdam [Amsterdam] (UvA), Department of rheumatology, Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden, Rheumatology Unit, Department of Medicine, University of California [San Francisco] (UC San Francisco), University of California (UC), Rheumatology Unit, Karolinska Institutet [Stockholm], Merck & Co. Inc, Structural Bioinformatics Group (GRIB), Barcelona Research Park of Biomedicine (PRBB), Universitat Pompeu Fabra [Barcelona] (UPF), Capital Normal University [Beijing], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), MINES ParisTech - École nationale supérieure des mines de Paris, California Institute of Technology (CALTECH)-NASA, Department of Mechanical and Aerospace Engineering [Davis], University of California-University of California, Università degli Studi di Camerino (UNICAM), University of California [San Francisco] (UCSF), University of California, Sage Bionetworks, University of Michigan, Ann Arbor, Pompeu Fabra University, Icahn School of Medicine at Mount Sinai, Corrona LLC, Northeastern University, Harvard University, University of Lisbon, IBM, INSERM U900, University of Helsinki, University of Toronto, Scripps Research Institute, Medical University of Vienna, University of Texas at Dallas, New York University, Albany Medical College, Arthritis Research Center Foundation, Radboud University Nijmegen, INSERM U1184, University of Amsterdam, Glaxo Smith Kline, Leiden University, University of Alabama at Birmingham, University of California San Francisco, University of Pittsburgh, Karolinska Institutet, North Shore-Long Island Jewish Health System, Merck, Aalto-yliopisto, and Aalto University

Subjects
Male, 0301 basic medicine, General Physics and Astronomy, Arthritis, Genome-wide association study, Bioinformatics, DISEASE, Arthritis, Rheumatoid, Cohort Studies, Missing heritability problem, MISSING HERITABILITY, Medicine, Certolizumab pegol, RISK, Multidisciplinary, Antibodies, Monoclonal, Middle Aged, Prognosis, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, STACKED GENERALIZATION, Treatment Outcome, Antirheumatic Agents, Crowdsourcing, Biomarker (medicine), Female, Erratum, medicine.drug, Adult, Science, Context (language use), Antibodies, Monoclonal, Humanized, Polymorphism, Single Nucleotide, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, INFLIXIMAB, Journal Article, Humans, SNP, Genetic Predisposition to Disease, GENOME-WIDE ASSOCIATION, METAANALYSIS, Aged, ta113, Tumor Necrosis Factor-alpha, business.industry, NETWORK INFERENCE, COMPLEX TRAITS, Artritis reumatoide -- Tractament, CLINICAL-RESPONSE, General Chemistry, 113 Computer and information sciences, medicine.disease, Infliximab, 030104 developmental biology, 3121 General medicine, internal medicine and other clinical medicine, Certolizumab Pegol, business, RC
Abstract

Rheumatoid arthritis (RA) affects millions world-wide. While anti-TNF treatment is widely used to reduce disease progression, treatment fails in ∼one-third of patients. No biomarker currently exists that identifies non-responders before treatment. A rigorous community-based assessment of the utility of SNP data for predicting anti-TNF treatment efficacy in RA patients was performed in the context of a DREAM Challenge (http://www.synapse.org/RA_Challenge). An open challenge framework enabled the comparative evaluation of predictions developed by 73 research groups using the most comprehensive available data and covering a wide range of state-of-the-art modelling methodologies. Despite a significant genetic heritability estimate of treatment non-response trait (h2=0.18, P value=0.02), no significant genetic contribution to prediction accuracy is observed. Results formally confirm the expectations of the rheumatology community that SNP information does not significantly improve predictive performance relative to standard clinical traits, thereby justifying a refocusing of future efforts on collection of other data., Rheumatoid arthritis patients respond differently to anti-TNF treatment. Using community-based challenge, the authors show that currently available data does not reveal meaningful genetic predictors of response to anti-TNF therapy, thus confirming clinical observations.

Published
2016

10. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Author

Seunghee Lee, Jetty S.S. Ammiraju, Railson Schreinert dos Santos, Ann Danowitz, Shu-Min Kao, Li Zhang, Chengjun Zhang, Cheng chieh Wu, Dongying Gao, Carlos E.M. Londono, Scott A. Jackson, Yi Liao, Mingsheng Chen, Chuanzhu Fan, Andrea Zuccolo, Muhua Wang, Christos Noutsos, Rod A. Wing, Manyuan Long, Robert J Henry, Marie-Christine Carpentier, Kshirod K. Jena, Aiko Iwata, Yue-Ie C. Hsing, Jose Luis Goicoechea, Bin Han, Richard Cooke, Joshua C. Stein, Luis F. Rivera, Thomas Wicker, Dario Copetti, Fu Jin Wei, Claude Becker, Paul L. Sanchez, Qi Feng, Andrea R. Gschwend, Ramil Mauleon, Carlos A. Machado, Derrick J. Zwickl, Daniel da Rosa Farias, Jayson Talag, Dave Flowers, Eric Lasserre, Nickolai Alexandrov, Yeisoo Yu, Moaine El Baidouri, Luciano Carlos da Maia, Jeremy Schmutz, Dave Kudrna, Olivier Panaud, Kenneth L. McNally, Xiang Song, Kevin G. Nyberg, Nori Kurata, Qiang Zhao, Kapeel Chougule, Jhih wun Zeng, Antonio Costa de Oliveira, Jianwei Zhang, Doreen Ware, Jun Wang, Detlef Weigel, Sharon Wei, Julie Jacquemin, Michael J. Sanderson, Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, Dipartimento Sci Agr & Ambientali, Università degli Studi di Udine - University of Udine [Italie], Wuhan University [China], University of Georgia [USA], Chinese Academy of Agricultural Mechanization Sciences (CCCME), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Tsukuba University of Technology, Graduate School of Comprehensive Human Sciences, Université de Tsukuba = University of Tsukuba, Sismologie (IPGS) (IPGS-Sismologie), Institut de physique du globe de Strasbourg (IPGS), Université de Strasbourg (UNISTRA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), United States Department of Energy, Institute of Plant Biology, University of Zurich, Plant Genomics and Breeding Center, Department of Biology, and Cold Spring Harbor Laboratory

Subjects
0301 basic medicine, Crops, Agricultural, Evolution, Genetic Speciation, [SDV]Life Sciences [q-bio], Plant genetics, Introgression, Genomics, Crops, Oryza, Genome, Medical and Health Sciences, Evolution, Molecular, Domestication, 03 medical and health sciences, Molecular evolution, Phylogenetics, Genetics, ComputingMilieux_MISCELLANEOUS, Phylogeny, Conserved Sequence, 2. Zero hunger, Agricultural, biology, food and beverages, Molecular, Genetic Variation, Plant, 15. Life on land, Biological Sciences, biology.organism_classification, 030104 developmental biology, Evolutionary biology, Genome, Plant, Developmental Biology
Abstract

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.

Published
2018

11. Transposons: a blessing curse

Author

Dubin, Manu, Scheid, Ortrun, Becker, Claude, Laboratoire de Génétique et Evolution des Populations Végétales, Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS), Gregor Mendel Institute of Molecular Plant Biology (GMI), and Austrian Academy of Sciences (OeAW)

Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, food and beverages, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics
Abstract

International audience; The genomes of most plant species are dominated by transposable elements (TEs). Once considered as ‘junk DNA’, TEs are now known to have a major role in driving genome evolution. Over the last decade, it has become apparent that some stress conditions and other environmental stimuli can drive bursts of activity of certain TE families and consequently new TE insertions. These can give rise to altered gene expression patterns and phenotypes, with new TE insertions sometimes causing flanking genes to become transcriptionally responsive to the same stress conditions that activated the TE in the first place. Such connections between TE-mediated increases in diversity and an accelerated rate of genome evolution provide powerful mechanisms for plants to adapt more rapidly to new environmental conditions. This review will focus on environmentally induced transposition, the mechanisms by which it alters gene expression, and the consequences for plant genome evolution and breeding.

Published
2018

12. Transposons: a blessing curse

Author

Dubin, Manu J, Mittelsten Scheid, Ortrun, Becker, Claude, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), and Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP))

Subjects
[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

13. The rate and potential relevance of new mutations in a colonizing plant lineage

Author

Verena J. Schuenemann, Jia-Hui Chen, Rob W. Ness, Wolfgang Busch, Dominik G. Grimm, Hernán A. Burbano, Claude Becker, Radka Slovak, Benjamin Brachi, Claudia Setzer, Johannes Krause, Joy Bergelson, Ella Reiter, Detlef Weigel, Moises Exposito-Alonso, Joerg Hagmann, Max-Planck-Institut, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Chinese Academy of Sciences (CAS), Department of Ecology and Evolution [Chicago], University of Chicago, Department of Biology, and Northern Arizona University [Flagstaff]

Subjects
0301 basic medicine, 0106 biological sciences, Cancer Research, Mutation rate, [SDV]Life Sciences [q-bio], Arabidopsis, Population genetics, Plant Weeds, Plant Science, medicine.disease_cause, Plant Genetics, méthode de croisement, 01 natural sciences, Genome, Gene flow, Negative selection, Mutation Rate, Plant Genomics, amérique du nord, Genetics (clinical), Phylogeny, Data Management, Mutation, 0303 health sciences, Natural selection, Chemical Reactions, Eukaryota, Phylogenetic Analysis, Genomics, Plants, Phylogenetics, Chemistry, Phenotype, Experimental Organism Systems, Physical Sciences, Genome, Plant, Research Article, Biotechnology, Gene Flow, Computer and Information Sciences, Substitution Mutation, Lineage (genetic), lcsh:QH426-470, Plant Development, Brassica, Biology, Research and Analysis Methods, Methylation, 010603 evolutionary biology, Evolution, Molecular, 03 medical and health sciences, Model Organisms, Plant and Algal Models, medicine, Genetics, Evolutionary Systematics, Selection, Genetic, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Crosses, Genetic, Selection (genetic algorithm), Taxonomy, 030304 developmental biology, Evolutionary Biology, Population Biology, arabidopsis thaliana, Organisms, Biology and Life Sciences, Computational Biology, Selfing, Sequence Analysis, DNA, Genome Analysis, Genomic Libraries, Genome Annotation, lcsh:Genetics, 030104 developmental biology, Evolutionary biology, Plant Biotechnology, Directed Molecular Evolution, Introduced Species, Population Genetics
Abstract

By following the evolution of populations that are initially genetically homogeneous, much can be learned about core biological principles. For example, it allows for detailed studies of the rate of emergence of de novo mutations and their change in frequency due to drift and selection. Unfortunately, in multicellular organisms with generation times of months or years, it is difficult to set up and carry out such experiments over many generations. An alternative is provided by “natural evolution experiments” that started from colonizations or invasions of new habitats by selfing lineages. With limited or missing gene flow from other lineages, new mutations and their effects can be easily detected. North America has been colonized in historic times by the plant Arabidopsis thaliana, and although multiple intercrossing lineages are found today, many of the individuals belong to a single lineage, HPG1. To determine in this lineage the rate of substitutions—the subset of mutations that survived natural selection and drift–, we have sequenced genomes from plants collected between 1863 and 2006. We identified 73 modern and 27 herbarium specimens that belonged to HPG1. Using the estimated substitution rate, we infer that the last common HPG1 ancestor lived in the early 17th century, when it was most likely introduced by chance from Europe. Mutations in coding regions are depleted in frequency compared to those in other portions of the genome, consistent with purifying selection. Nevertheless, a handful of mutations is found at high frequency in present-day populations. We link these to detectable phenotypic variance in traits of known ecological importance, life history and growth, which could reflect their adaptive value. Our work showcases how, by applying genomics methods to a combination of modern and historic samples from colonizing lineages, we can directly study new mutations and their potential evolutionary relevance., PLoS Genetics, 14 (2), ISSN:1553-7390, ISSN:1553-7404

Published
2018

14. Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome

Author

Akifumi Sugiyama, Efraín De Luna, Hideya Fukuzawa, Yuki Hirakawa, Yoshihiro Yoshitake, Jeremy Schmutz, Minoru Kubo, Sabine Zachgo, Sumio Sugano, Satoshi Naramoto, Isabel Monte, Juan Caballero-Pérez, Takashi Okamoto, Feng Chen, Keita Kinose, Rui Sun, Bruno Catarino, Shin-ichiro Inoue, Tomokazu Kawashima, Yasukazu Nakamura, Masaaki Umeda, Masayuki Tsuzuki, Junko Kyozuka, John L. Bowman, Mitsuru Kakita, Chia-Wei Lu, Eduardo Flores-Sandoval, Takayuki Kohchi, Christian R. Boehm, Kimitsune Ishizaki, D. Magnus Eklund, Shih-Shun Lin, Makoto Shirakawa, Jim Haseloff, Moritz Rövekamp, Hirofumi Nakagami, Anna Lipzen, Yuichiro Watanabe, Kazuhiko Nishitani, Noriyuki Suetsugu, Keisuke Inoue, Marc W. Schmid, Yosuke Kawai, Hirokazu Tomogane, Robert A. Martienssen, Shengqiang Shu, Ryuichi Nishihama, Ulf Lagercrantz, Miya Mizutani, Liam Dolan, Tom Dierschke, Frédéric Berger, Felix Althoff, Kevin M. Davies, Ueli Grossniklaus, Bence Galik, Asao Fujiyama, Sureshkumar Balasubrmanian, Ryusuke Yokoyama, Takashi Ueda, Izumi Yotsui, Toshinori Kinoshita, Misato Ohtani, Eri Koide, Kazufumi Yazaki, Shinichiro Sawa, Jane Grimwood, Diane Bauer, Mario A. Arteaga-Vazquez, Sakiko Ishida, Takahiro Hamada, Roberto Solano, Alexander J. Hetherington, Daniel Grimanelli, Stevie N. Florent, Erika Lindquist, Ryosuke Sano, Kenji Komatsu, Catherine Adam, Asuka Higo, Sarah Kopischke, Hope Hundley, Rebecca A. Mosher, Jerry Jenkins, Naoki Minamino, Hideki Nagasaki, Mizuki Takenaka, Kerrie Barry, Takashi Araki, Nobuyoshi Mochizuki, Anke Reinders, Mihails Delmans, Yuji Kohara, Yoko Ikeda, Daisuke Takezawa, Mansi Chovatia, Ana E. Dorantes-Acosta, Taku Demura, Masaki Okumura, Qidong Jia, Takehiko Kanazawa, Yutaka Suzuki, Megan Kennedy, Jeremy Phillips, Bernardo Pollak, Liam N. Briginshaw, Shohei Yamaoka, Shota Chiyoda, Alexander Spunde, John M. Ward, Masaharu Mizutani, Katsuyuki T. Yamato, Shiori S Aki, Boehm, Christian [0000-0002-6633-7998], Haseloff, Jim [0000-0003-4793-8058], Pollak, Bernardo [0000-0003-2329-7401], Apollo - University of Cambridge Repository, Monash University [Clayton], Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Kobe University, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Nara Institute of Science and Technology, Monash University [Melbourne], The University of Tennessee [Knoxville], Osnabrück University of Applied Sciences (OS UAS), Hochschule Osnabrück, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Earth Science and Astrononomy [Tokyo], The University of Tokyo (UTokyo), National Institute for Basic Biology [Okazaki] (NIBB), Graduate University for Advanced Studies [Hayama] (SOKENDAI), Cold Spring Harbor Laboratory (CSHL), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Max Planck Institute for Plant Breeding Research (MPIPZ), Tokyo Metropolitan University [Tokyo] (TMU), Kumamoto University, Biocomputing Unit [Madrid], Research Institute for Sustainable Humanosphere (RISH), Kyoto University [Kyoto], University of Ulm (UUlm), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Kyoto University

Subjects
inorganic chemicals, 0301 basic medicine, Flora, Transcription, Genetic, [SDV]Life Sciences [q-bio], Marchantia polymorpha, Adaptation, Biological, macromolecular substances, Genome, General Biochemistry, Genetics and Molecular Biology, Evolutionsbiologi, 03 medical and health sciences, Gene Expression Regulation, Plant, Botany, Marchantia, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, sex chromosome, Biological sciences, Plant evolution, Medical And Health Sciences, Evolutionary Biology, biology, Ecology, fungi, food and beverages, Molecular Sequence Annotation, Biological evolution, Biological Sciences, 15. Life on land, biology.organism_classification, charophycean algae, Biological Evolution, 030104 developmental biology, Embryophyta, Terrestrial ecosystem, land plant evolution, auxin, Genome, Plant, Developmental Biology, Signal Transduction
Abstract

The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant., 陸上植物の祖先の特徴をもつ苔類ゼニゴケの全ゲノム構造を解明. 京都大学プレスリリース. 2017-10-06.

Published
2017

15. Patterns of Polymorphism at the Self-Incompatibility Locus in 1,083 Arabidopsis thaliana Genomes

Author

Isabelle Fobis-Loisy, Xavier Vekemans, Vincent Castric, Quan Long, Magnus Nordborg, Pauline M. Goubet, Anne-Catherine Holl, Elisa Prat, Dazhe Meng, Takashi Tsuchimatsu, Alexander Platzer, William Marande, Hélène Bergès, Sophie Gallina, Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Department of Biology, Chiba University, Inage-ku, Chiba, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Lab Reprod & Dev Plantes, École normale supérieure - Lyon (ENS Lyon), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Gregor Mendel Institute (GMI) - Vienna Biocenter (VBC), Austrian Academy of Sciences (OeAW), University of Calgary, Gregor Mendel Institute of Molecular Plant Biology (GMI), JSPS KAKENHI [15K18583], ANR-11-BSV7-013-03, ANR-11-JSV7-008-01, European Research Council [648321], ANR-13-BSV7-0013,BugsInACell,Accommodation intracellulaire des bactéries symbiotiques fixatrices d'azote(2013), ANR-13-JSV7-0003,DOMEVOL,Mecanismes et evolution de la dominance(2013), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and École normale supérieure de Lyon (ENS de Lyon)

Subjects
0106 biological sciences, evolution of selfing, Arabidopsis, Locus (genetics), Self-Fertilization, Biology, Genes, Plant, 01 natural sciences, Genome, self-incompatibility, Haplogroup, Evolution, Molecular, 03 medical and health sciences, 1001 genomes project, evolutionary transition, Amino Acid Sequence, Alleles, Phylogeny, Discoveries, ComputingMilieux_MISCELLANEOUS, Plant Proteins, 030304 developmental biology, Genetics, 0303 health sciences, Polymorphism, Genetic, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Arabidopsis Proteins, Haplotype, Breakpoint, Selfing, 15. Life on land, Fixation (population genetics), Haplotypes, Mutation, Recombination, 010606 plant biology & botany
Abstract

Although the transition to selfing in the model plantArabidopsis thalianainvolved the loss of the self-incompatibility (SI) system, it clearly did not occur due to the fixation of a single inactivating mutation at the locus determining the specificities of SI (the S-locus). At least three groups of divergent haplotypes (haplogroups), corresponding to ancient functional S-alleles, have been maintained at this locus, and extensive functional studies have shown that all three carry distinct inactivating mutations. However, the historical process of loss of SI is not well understood, in particular its relation with the last glaciation. Here, we took advantage of recently published genomic re-sequencing data in 1,083Arabidopsis thalianaaccessions that we combined with BAC sequencing to obtain polymorphism information for the whole S-locus region at a species-wide scale. The accessions differed by several major rearrangements including large deletions and inter-haplogroup recombinations, forming a set of haplogroups that are widely distributed throughout the native range and largely overlap geographically. ‘Relict’A.thalianaaccessions that directly derive from glacial refugia are polymorphic at the S-locus, suggesting that the three haplogroups were already present when glacial refugia from the last Ice Age became isolated. Inter-haplogroup recombinant haplotypes were highly frequent, and detailed analysis of recombination breakpoints suggested multiple independent origins. These findings suggest that the complete loss of SI inA.thalianainvolved independent self-compatible mutants that arose prior to the last Ice Age, and experienced further rearrangements during post-glacial colonization.

Published
2017

16. Zinc availability modulates plant growth and 1 immune responses via AZI1

Author

Bouain, Nadia, Satbhai, Santosh B., Saenchai, Chorpet, Desbrosses, Guilhem, Berthomieu, Pierre, Busch, Wolfgang, Rouached, Hatem, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Space Research Institute of Austrian Academy of Sciences (IWF), Vienna Biocenter, Biochimie et Physiologie Moléculaire des Plantes ( BPMP ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Equipe Hormones, Nutriments et Développement (HoNuDe) ( HONUDE ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Austrian Academy of Sciences, Equipe Electrophysiologie de la nutrition minérale et des symbioses racinaires ( ELSA ), Equipe Adaptation des plantes aux métaux ( METAUX ), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Equipe Hormones, Nutriments et Développement (HoNuDe) (HONUDE), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Equipe Electrophysiologie de la nutrition minérale et des symbioses racinaires (ELSA), and Equipe Adaptation des plantes aux métaux (METAUX)

Subjects
[ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, acide azelaique, croissance racinaire, nonanedioic acid, arabidopsis thaliana, zinc, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, carence en zinc, régulation de la croissance
Abstract

preprint déposé dans bioRxiv; Zinc is an essential micronutrient for all living organisms and is involved in a plethora of processes including growth and development, and immunity. However, it is unknown if there is a common genetic and molecular basis underlying multiple facets of zinc function. Here we used natural variation in Arabidopsis thaliana to study the role of zinc in regulating growth. We identify allelic variation of the systemic immunity gene AZI1 as a key for determining root growth responses to low zinc conditions. We further demonstrate that this gene is important for modulating root growth depending on the zinc and defence status. Finally, we show that the interaction of the immunity signal azelaic acid and zinc level to regulate root growth is conserved in rice. This work demonstrates that there is a common genetic and molecular basis for multiple zinc dependent processes and that nutrient cues can determine the balance of plant growth and immune responses in plants.

Published
2017

17. Ecological plant epigenetics: Evidence from model and non-model species, and the way forward

Author

Sonja J. Prohaska, Koen J. F. Verhoeven, Claude Becker, Marie Mirouze, Christina L. Richards, Peter F. Stadler, Etienne Bucher, Christian Lampei, Walter Durka, Lars Opgenoorth, Emiliano Trucchi, Jan Engelhardt, Ovidiu Paun, Conchita Alonso, Bence Gáspár, Stefan A. Rensing, Ilkka Kronholm, Vít Latzel, Maria Colomé-Tatché, Kristian K. Ullrich, Andreas Gogol-Döring, Thomas P. van Gurp, Katrin Heer, Oliver Bossdorf, Ivo Grosse, University of South Florida [Tampa] (USF), Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Plant Evolutionary Ecology, University of Tübingen, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, European Research Institute for the Biology of Ageing [Groningen] (ERIBA), University Medical Center Groningen [Groningen] (UMCG), Helmholtz Zentrum München = German Research Center for Environmental Health, TUM School of Life Sciences Weihenstephan, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), German Centre for Integrative Biodiversity Research (iDiv), Institut für Informatik [Leipzig], Universität Leipzig, Institut für Informatik / Institute of Computer Science [Halle], Martin-Luther-University Halle-Wittenberg, Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Philipps Universität Marburg = Philipps University of Marburg, University of Jyväskylä (JYU), Institute of Plant Breeding, Seed Science and Population Genetics, Universität Hohenheim, Institute of Botany of the Czech Academy of Sciences (IB / CAS), Czech Academy of Sciences [Prague] (CAS), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Department of Botany and Biodiversity Research, University of Vienna [Vienna], Santa Fe Institute, Centre for Biological Signaling Studies [Freiburg] (BIOSS), University of Freiburg [Freiburg], Max Planck Institute for Mathematics in the Sciences (MPI-MiS), Max-Planck-Gesellschaft, Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Laboratoire de Physique Théorique et Modèles Statistiques (LPTMS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Helmholtz Zentrum für Umweltforschung (UFZ), Inst Comp Sci, Martin-Luther-Universität Halle Wittenberg (MLU), Institute of Experimental Ecology Germany, Conservation Biology and Ecology, Universität Ulm - Ulm University [Ulm, Allemagne], Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Carl-Maria-von-Weber-Gesamtausgabe, Universität Paderborn (UPB), Department of Zoology [Oxford], University of Oxford [Oxford], Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11), and Terrestrial Ecology (TE)

Subjects
0106 biological sciences, 0301 basic medicine, EPIGENOMIC DIVERSITY, [SDV]Life Sciences [q-bio], Species distribution, INDIVIDUAL VARIATION, Phenotypic plasticity, 01 natural sciences, Genome, phenotypic plasticity, Epigenesis, Genetic, DNA METHYLATION VARIATION, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Ecology, bioinformatiikka, genomiikka, Genomics, Plants, Bioinformatics, ecological epigenetics, genomics, response to environment, Ecology, Evolution, Behavior and Systematics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Habitat, epigenetiikka, international, PHYSCOMITRELLA-PATENS, PERENNIAL HERB, kasviekologia, Ecological epigenetics, SEQUENCING DATA, Evolution, Ecology (disciplines), Biology, 010603 evolutionary biology, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Polyploid, Behavior and Systematics, kasvit, Epigenetics, Ecosystem, 030304 developmental biology, HERB HELLEBORUS-FOETIDUS, Ecological Epigenetics, Phenotypic Plasticity, Response To Environment, Ambientale, Response to environment, DNA Methylation, 15. Life on land, Ecological realism, Plant ecology, 030104 developmental biology, ARABIDOPSIS-THALIANA, Bioinformatics, ecological epigenetics, genomics, phenotypic plasticity, response to environment, Adaptation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, NATURAL-POPULATIONS
Abstract

Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute to a more mechanistic understanding but have limited ecological realism. Understanding the significance of epigenetics for plant ecology requires increased transfer of knowledge and methods from model species research to genomes of evolutionarily divergent species, and examination of responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration among molecular geneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.

Published
2017

18. Live-cell analysis of DNA methylation during sexual reproduction in Arabidopsis reveals context and sex-specific dynamics controlled by noncanonical RdDM

Author

Benjamin Selles, Matthias Van Durme, Robert A. Martienssen, Andrea J. Schorn, Frédéric Berger, Daphné Autran, Moritz K. Nowack, Caroline Michaud, Thiet Minh Vu, Daniel Grimanelli, Mathieu Ingouff, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Cold Spring Harbor Laboratory (CSHL), Universiteit Gent = Ghent University (UGENT), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Universiteit Gent = Ghent University [Belgium] (UGENT)

Subjects
0301 basic medicine, CHROMATIN, EPIGENETIC INHERITANCE, Arabidopsis, ENDOSPERM, Biology, sensors, DEMETHYLATION, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, Cell Line, HETEROCHROMATIN, reproduction, 03 medical and health sciences, Mice, Epigenetics of physical exercise, Sex Factors, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Histone methylation, Genetics, Animals, Epigenetics, PLANT, RNA-Directed DNA Methylation, Embryonic Stem Cells, Epigenomics, SMALL RNA, EARLY EMBRYOGENESIS, DNA methylation, THALIANA, Arabidopsis Proteins, Reproduction, Biology and Life Sciences, reprogramming, Methylation, DNA-Directed RNA Polymerases, Methyltransferases, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, DNA Methylation, Plants, Genetically Modified, GENOME, 030104 developmental biology, Gene Expression Regulation, Single-Cell Analysis, Reprogramming, Resource/Methodology, Developmental Biology
Abstract

Cytosine methylation is a key epigenetic mark in many organisms, important for both transcriptional control and genome integrity. While relatively stable during somatic growth, DNA methylation is reprogrammed genome-wide during mammalian reproduction. Reprogramming is essential for zygotic totipotency and to prevent transgenerational inheritance of epimutations. However, the extent of DNA methylation reprogramming in plants remains unclear. Here, we developed sensors reporting with single-cell resolution CG and non-CG methylation in Arabidopsis. Live imaging during reproduction revealed distinct and sex-specific dynamics for both contexts. We found that CHH methylation in the egg cell depends on DOMAINS REARRANGED METHYLASE 2 (DRM2) and RNA polymerase V (Pol V), two main actors of RNA-directed DNA methylation, but does not depend on Pol IV. Our sensors provide insight into global DNA methylation dynamics at the single-cell level with high temporal resolution and offer a powerful tool to track CG and non-CG methylation both during development and in response to environmental cues in all organisms with methylated DNA, as we illustrate in mouse embryonic stem cells.

Published
2017

19. Nonsense-Mediated mRNA Decay Modulates Immune Receptor Levels to Regulate Plant Antibacterial Defense

Author

Arunkumar Srinivasan, Bettina Dekrout, Claudia Jonak, Nina Riehs, Svetlana Akimcheva, Karel Riha, Branislav Kusenda, Jane E. Parker, José M. Jiménez-Gómez, Jaqueline Bautor, Jiradet Gloggnitzer, Hansjörg Stampfl, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), Department of Plant-Microbe Interactions, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, CEITEC, Masaryk University, Austrian Academy of Sciences, Austrian Science Fund ( P19256-B03), Max-Planck Society, Deutsche Forschungsgemeinschaft (SFB 680), and Masaryk University [Brno] (MUNI)

Subjects
Cancer Research, binding, disease resistance, growth, [SDV]Life Sciences [q-bio], Nonsense-mediated decay, Pseudomonas syringae, Immune receptor, Biology, Microbiology, Immune system, Virology, Arabidopsis, Immunology and Microbiology(all), Gene expression, RNA, Messenger, Receptors, Immunologic, Gene, Molecular Biology, Plant Diseases, Genetics, Innate immune system, Arabidopsis Proteins, upf1, biology.organism_classification, encoding genes, gene-expression, inhibition, Nonsense Mediated mRNA Decay, arabidopsis, Codon, Nonsense, Host-Pathogen Interactions, human-cells, Parasitology, nmd, Signal transduction, Carrier Proteins, RNA Helicases
Abstract

SummaryNonsense-mediated mRNA decay (NMD) is a conserved eukaryotic RNA surveillance mechanism that degrades aberrant mRNAs. NMD impairment in Arabidopsis is linked to constitutive immune response activation and enhanced antibacterial resistance, but the underlying mechanisms are unknown. Here we show that NMD contributes to innate immunity in Arabidopsis by controlling the turnover of numerous TIR domain-containing, nucleotide-binding, leucine-rich repeat (TNL) immune receptor-encoding mRNAs. Autoimmunity resulting from NMD impairment depends on TNL signaling pathway components and can be triggered through deregulation of a single TNL gene, RPS6. Bacterial infection of plants causes host-programmed inhibition of NMD, leading to stabilization of NMD-regulated TNL transcripts. Conversely, constitutive NMD activity prevents TNL stabilization and impairs plant defense, demonstrating that host-regulated NMD contributes to disease resistance. Thus, NMD shapes plant innate immunity by controlling the threshold for activation of TNL resistance pathways.

Published
2014
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20. Brassinosteroid-regulated GSK3/Shaggy-like Kinases Phosphorylate Mitogen-activated Protein (MAP) Kinase Kinases, Which Control Stomata Development in Arabidopsis thaliana

Author

Jean Bigeard, Sigrid Husar, Brigitte Poppenberger, Mamoona Khan, Wilfried Rozhon, Delphine Pflieger, Markus Teige, Andrea Pitzschke, Claudia Jonak, Heribert Hirt, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), University of Vienna [Vienna], Unité de recherche en génomique végétale (URGV), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Cergy Pontoise (UCP), Université Paris-Seine-Université Paris-Seine-Université d'Évry-Val-d'Essonne (UEVE)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), King Saud University [Riyadh] (KSU), Université Paris-Seine-Université Paris-Seine-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), University of Natural Resources and Life Sciences (BOKU), Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE - UMR 8587), and Université Paris-Seine-Université Paris-Seine-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
cell division, Enzymologic, 0106 biological sciences, MAPK/ERK pathway, Arabidopsis thaliana, Mitogen-Activated Protein Kinase 3, Arabidopsis, Plant Biology, Mitogen activated protein kinase, 01 natural sciences, Biochemistry, Plants (botany), enzyme repression, Glycogen Synthase Kinase 3, chemistry.chemical_compound, Gene Expression Regulation, Plant, Models, Brassinosteroid, BIN2 protein, enzyme phosphorylation, Cloning, Molecular, cell elongation, Phosphorylation, Cell proliferation, Glutathione Transferase, cell fate, 0303 health sciences, biology, Kinase, Plant Stomata, article, food and beverages, protein function, Plants, Plants, Genetically Modified, Recombinant Proteins, Enzymes, unclassified drug, enzyme activity, Cell biology, priority journal, Over-expression, protein protein interaction, Mitogen-activated protein kinase, Steroids, plant development, wild type, hormone action, Signal Transduction, animal structures, Cell divisions, in vitro study, Cells, Genetically Modified, macromolecular substances, Cell fate determination, plant stoma, Models, Biological, Gene Expression Regulation, Enzymologic, in vivo study, 03 medical and health sciences, Genetic, Brassinosteroids, Escherichia coli, controlled study, Environmental cues, Cell fate decision, protein expression, Molecular Biology, Steroid hormones, 030304 developmental biology, Mitogen-Activated Protein Kinase Kinases, nonhuman, Models, Genetic, Arabidopsis protein, fungi, Molecular, Plant, Cell Biology, Biological, biology.organism_classification, mitogen activated protein kinase 3, mitogen activated protein kinase kinase 4, mitogen activated protein kinase kinase 5, Gene Expression Regulation, chemistry, brassinosteroid, mitogen activated protein kinase 6, biology.protein, [PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph], Cytology, Cloning, 010606 plant biology & botany
Abstract

International audience; Brassinosteroids (BRs) are steroid hormones that coordinate fundamental developmental programs in plants. In this study we show that in addition to the well established roles of BRs in regulating cell elongation and cell division events, BRs also govern cell fate decisions during stomata development in Arabidopsis thaliana. In wild-type A. thaliana, stomatal distribution follows the one-cell spacing rule; that is, adjacent stomata are spaced by at least one intervening pavement cell. This rule is interrupted in BR-deficient and BR signaling-deficient A. thaliana mutants, resulting in clustered stomata. We demonstrate that BIN2 and its homologues, GSK3/Shaggy-like kinases involved in BR signaling, can phosphorylate the MAPK kinases MKK4 and MKK5, which are members of the MAPK module YODA-MKK4/5-MPK3/6 that controls stomata development and patterning. BIN2 phosphorylates a GSK3/Shaggy-like kinase recognition motif in MKK4, which reduces MKK4 activity against its substrate MPK6 in vitro. In vivo we show that MKK4andMKK5act downstream of BR signaling because their overexpression rescued stomata patterning defects in BR-deficient plants. A model is proposed in which GSK3-mediated phosphorylation of MKK4 and MKK5 enables for a dynamic integration of endogenous or environmental cues signaled by BRs into cell fate decisions governed by the YODA-MKK4/5-MPK3/6 module.

Published
2013

21. Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging

Author

Stephanie Werner, Lijuan Zhang, Thomas Greb, Yvon Jaillais, Kareem Elsayad, Jixiang Kong, Edmundo R. Sánchez Guajardo, Marçal Gallemí, Youssef Belkhadir, Vienna Biocenter Core Facilities, Partenaires INRAE, Austrian Academy of Sciences (OeAW), University Medical Center Göttingen (UMG), Gregor Mendel Institute of Molecular Plant Biology (GMI), Institute of Science and Technology [Austria] (IST Austria), Vienna Biocenter, Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Centre for Organismal Studies, Universität Heidelberg [Heidelberg], Austrian Federal Ministry of Science, Research Economy, City of Vienna through the VBCF, Austrian Academy of Science through the Gregor Mendel Institute, Austrian Science Fund (FWF) P25594-168 B21, German Research Foundation (DFG) GR 2104/4-1, Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), and Universität Heidelberg [Heidelberg] = Heidelberg University

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], Hydrostatic pressure, Arabidopsis, 01 natural sciences, Biochemistry, 010309 optics, Extracellular matrix, 03 medical and health sciences, 0103 physical sciences, Extracellular, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, biology, Chemistry, Cell Biology, biology.organism_classification, Cell biology, Extracellular Matrix, Multicellular organism, 030104 developmental biology, Microscopy, Fluorescence, Cytoplasm, Mutation, Signal transduction, Developmental biology
Abstract

International audience; Extracellular matrices (ECMs) are central to the advent of multicellular life, and their mechanical properties are modulated by and impinge on intracellular signaling pathways that regulate vital cellular functions. High spatial-resolution mapping of mechanical properties in live cells is, however, extremely challenging. Thus, our understanding of how signaling pathways process physiological signals to generate appropriate mechanical responses is limited. We introduce fluorescence emission-Brillouin scattering imaging (FBi), a method for the parallel and all-optical measurements of mechanical properties and fluorescence at the submicrometer scale in living organisms. Using FBi, we showed that changes in cellular hydrostatic pressure and cytoplasm viscoelasticity modulate the mechanical signatures of plant ECMs. We further established that the measured "stiffness" of plant ECMs is symmetrically patterned in hypocotyl cells undergoing directional growth. Finally, application of this method to Arabidopsis thaliana with photoreceptor mutants revealed that red and far-red light signals are essential modulators of ECM viscoelasticity. By mapping the viscoelastic signatures of a complex ECM, we provide proof of principle for the organism-wide applicability of FBi for measuring the mechanical outputs of intracellular signaling pathways. As such, our work has implications for investigations of mechanosignaling pathways and developmental biology.

Published
2016

22. Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids

Author

Claude Becker, Detlef Weigel, Mélanie Rigal, Yoko Ikeda, Jane Devos, Romain Pogorelcnik, Olivier Mathieu, Thierry Pélissier, Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Genetics, Multidisciplinary, [SDV]Life Sciences [q-bio], food and beverages, Epigenome, Biology, 03 medical and health sciences, 030104 developmental biology, Epigenetics of physical exercise, PNAS Plus, DNA methylation, Epigenetics, Reprogramming, Transposons as a genetic tool, RNA-Directed DNA Methylation, ComputingMilieux_MISCELLANEOUS, Epigenomics
Abstract

Genes and transposons can exist in variable DNA methylation states, with potentially differential transcription. How these epialleles emerge is poorly understood. Here, we show that crossing an Arabidopsis thaliana plant with a hypomethylated genome and a normally methylated WT individual results, already in the F1 generation, in widespread changes in DNA methylation and transcription patterns. Novel nonparental and heritable epialleles arise at many genic loci, including a locus that itself controls DNA methylation patterns, but with most of the changes affecting pericentromeric transposons. Although a subset of transposons show immediate resilencing, a large number display decreased DNA methylation, which is associated with de novo or enhanced transcriptional activation and can translate into transposon mobilization in the progeny. Our findings reveal that the combination of distinct epigenomes can be viewed as an epigenomic shock, which is characterized by a round of epigenetic variation creating novel patterns of gene and TE regulation.

Published
2016

23. TDM1 Regulation Determines the Number of Meiotic Divisions

Author

Arp Schnittger, Hirofumi Harashima, Yuko Nomura, Laurence Cromer, Karel Riha, Sylvie Jolivet, Raphael Mercier, Wayne Crismani, Marta Cifuentes, Charlotte Renne, Keiko Sugimoto, Hirofumi Nakagami, Petra Bulankova, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, RIKEN Plant Science Center, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), University of Hamburg, Masaryk University [Brno] (MUNI), Czech Science Foundation [14-22346S], Japan Society for the Promotion of Science (JSPS) [26291064, 26650106, 15H01247], Fondation Simone et Cino del Duca, INRA BAP department, Labex Saclay Plant Sciences-SPS [ANR-10-LABX-0040-SPS], European Project: 281659,EC:FP7:ERC,ERC-2011-StG_20101109,MEIOSIGHT(2012), and Mercier, Raphaël

Subjects
0301 basic medicine, Cancer Research, [SDV]Life Sciences [q-bio], Arabidopsis, Genetic recombination, Biochemistry, Tubulin, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Cell Cycle and Cell Division, Post-Translational Modification, Phosphorylation, Genetics (clinical), Genes, Dominant, Genetics, biology, Chromosome Biology, Meiosis, Phosphothreonine, Cell Processes, Ploidy, Research Article, Protein Binding, lcsh:QH426-470, Haploidisation, Models, Biological, Anaphase-Promoting Complex-Cyclosome, Chromosomes, Plant, 03 medical and health sciences, Cyclin-dependent kinase, Cyclins, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Interkinesis, Telophase, Genetic Testing, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Metaphase, Arabidopsis Proteins, Meiosis II, Biology and Life Sciences, Proteins, Epistasis, Genetic, Cell Biology, Tetraploidy, lcsh:Genetics, Protein Subunits, 030104 developmental biology, Mutation, biology.protein, Anaphase, Peptides
Abstract

Cell cycle control must be modified at meiosis to allow two divisions to follow a single round of DNA replication, resulting in ploidy reduction. The mechanisms that ensure meiosis termination at the end of the second and not at the end of first division are poorly understood. We show here that Arabidopsis thaliana TDM1, which has been previously shown to be essential for meiotic termination, interacts directly with the Anaphase-Promoting Complex. Further, mutations in TDM1 in a conserved putative Cyclin-Dependant Kinase (CDK) phosphorylation site (T16-P17) dominantly provoked premature meiosis termination after the first division, and the production of diploid spores and gametes. The CDKA;1-CYCA1.2/TAM complex, which is required to prevent premature meiotic exit, phosphorylated TDM1 at T16 in vitro. Finally, while CYCA1;2/TAM was previously shown to be expressed only at meiosis I, TDM1 is present throughout meiosis. These data, together with epistasis analysis, lead us to propose that TDM1 is an APC/C component whose function is to ensure meiosis termination at the end of meiosis II, and whose activity is inhibited at meiosis I by CDKA;1-TAM-mediated phosphorylation to prevent premature meiotic exit. This provides a molecular mechanism for the differential decision of performing an additional round of division, or not, at the end of meiosis I and II, respectively., Author Summary Meiosis is a fundamental process for sexually reproducing organisms that creates genetic diversity within populations. A key feature of meiosis is the reduction of the number of chromosomes, from two sets to one set, prior to fertilization. This reduction in chromosome number is due to two cell divisions following a single round of DNA replication. In this study, we analysed the mechanism which controls the number of cell divisions, ensuring that meiotic termination occurs after the second meiotic division, and not at the end of the first division. We used the model plant Arabidopsis thaliana to show that the gene TDM1 has a central role in regulating meiotic cell divisions. The integrity of the gene affects whether one, two or three meiotic divisions will occur. We further explain the relationship between TDM1 and its regulator the cyclin TAM, and how they work together to produce reproductive cells with a reduced number of chromosomes. This tightly controlled mechanism ensures the transmission of the correct number of chromosomes from one generation to the next.

Published
2016

24. An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations

Author

Magnus Nordborg, Bjarni J. Vilhjálmsson, Alexander Platt, Ümit Seren, Quan Long, Vincent Segura, Arthur Korte, Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut National de la Recherche Agronomique (INRA), Austrian Academy of Sciences (OeAW), Gregor Mendel Institute of Molecular Plant Biology (GMI), Department of Molecular and Computational Biology, University of Southern California (USC), National Heart, Lung, and Blood Institute (NHLBI), Ecologie des Forets, Prairies et milieux Aquatiques (EFPA) department of INRA, Deutsche Forschungsgemeinschaft (DFG), US National Institutes of Health [P50 HG002790], European Union [283496], Austrian Academy of Sciences through GMI, Unité de recherche Amélioration, Génétique et Physiologie Forestières (UAGPF), Segura, Vincent, and Vilhjálmsson, Bjarni J

Subjects
0106 biological sciences, Mixed model, False discovery rate, Linkage disequilibrium, Genotype, Quantitative Trait Loci, Arabidopsis, Genome-wide association study, Locus (genetics), polymorphisme, Computational biology, Molecular Dynamics Simulation, Biology, mlst, Polymorphism, Single Nucleotide, 01 natural sciences, Article, Linkage Disequilibrium, apparentement, 03 medical and health sciences, Bayes' theorem, stratification, génétique d'association, Population Groups, Genetics, sélection, Humans, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, Genetic association, modèle mixte, 0303 health sciences, Vegetal Biology, Models, Genetic, Genome, Human, qtl, Chromosome Mapping, Bayes Theorem, variation génétique, régression, Genetic Loci, Allelic heterogeneity, étude d'association, Biologie végétale, Genome, Plant, Genome-Wide Association Study, 010606 plant biology & botany
Abstract

Population structure causes genome-wide linkage disequilibrium between unlinked loci, leading to statistical confounding in genome-wide association studies. Mixed models have been shown to handle the confounding effects of a diffuse background of large numbers of loci of small effect well, but do not always account for loci of larger effect. Here we propose a multi-locus mixed model as a general method for mapping complex traits in structured populations. Simulations suggest that our method outperforms existing methods, in terms of power as well as false discovery rate. We apply our method to human and Arabidopsis thaliana data, identifying novel associations in known candidates as well as evidence for allelic heterogeneity. We also demonstrate how a priori knowledge from an A. thaliana linkage mapping study can be integrated into our method using a Bayesian approach. Our implementation is computationally efficient, making the analysis of large datasets (n > 10000) practicable.

Published
2012

25. Tackling drought stress: receptor-like kinases present new approaches

Author

Aleksandra Skirycz, John Foulkes, Martin R. Broadley, Thomas Dresselhaus, Dominique Audenaert, Yvonne Stahl, Melinka A. Butenko, Thomas Greb, Tom Beeckman, Georg Felix, Alex Marshall, John P. Hammond, Sacco C. de Vries, Dirk Inzé, Michael Hothorn, Eugenia Russinova, Charlie Hodgman, Ueli Grossniklaus, Reidunn B. Aalen, Neil S. Graham, Christine Granier, Rüdiger Simon, Renze Heidstra, Ana I. Caño-Delgado, Cyril Zipfel, Lars Østergaard, Ive De Smet, University of Zurich, University of Nottingham, UK (UON), Department of Molecular Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Department of plant systems biology, Flanders Institute for Biotechnology, Department of Plant Biotechnology and Genetics, Universiteit Gent = Ghent University [Belgium] (UGENT), Division of Plant and Crop Sciences, School of Biosciences, Centre for Plant Integrative Biology, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Wageningen University and Research Centre (WUR), University of Regensburg, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Institute of Plant Biology and Zürich-Basel Plant Science Center, Universität Zürich [Zürich] = University of Zurich (UZH), Utrecht University [Utrecht], Max Planck Society, Biotechnology and Biological Sciences Research Council, Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], The Sainsbury Laboratory [Norwich] (TSL), Biological Science Research Council (BBSRC) [BB_BB/H022457/1, BB/G013969/1], Marie Curie European Reintegration Grant [PERG06-GA-2009-256354], Centre for BioSystems Genomics, Netherlands Genomics Initiative/Netherlands Organization for Scientific Research, Horizon grant, Netherlands Genomics Initiative/Netherlands Organization for Scientific Research [050-71-054], Marie-Curie Initial Training Network Bravissimo [PITN-GA-2008-215118, FP7-1-215118-2], Spanish Ministry of Education and Science [BIO2008/00505], Research Council of Norway [204756/F20], Interuniversity Attraction Poles Programme [IUAP VI/33], Belgian State, Science Policy Office, Human Frontier Science Program Organisation, Deutsche Forschungsgemeinshaft, Bundesministerium fur Ernahrung, Landwirtschaft und Verbraucherschutz, EuroCORES program, Gatsby Charitable Foundation, European Project: 215118,PEOPLE,FP7-PEOPLE-2007-1-1-ITN,BRAVISSIMO(2008), Universiteit Gent = Ghent University (UGENT), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Biotechnology and Biological Sciences Research Council (BBSRC)

Subjects
0106 biological sciences, Drought stress, Arabidopsis, Plant Science, 580 Plants (Botany), Biochemistry, 01 natural sciences, Plant Physiological Phenomena, 1307 Cell Biology, Plant Growth Regulators, 10126 Department of Plant and Microbial Biology, Gene Expression Regulation, Plant, 1110 Plant Science, Arabidopsis thaliana, 2. Zero hunger, 0303 health sciences, education.field_of_study, EPS-1, biology, Kinase, food and beverages, Droughts, Research Design, Perspective, abiotic stress, Population, Biochemie, arabidopsis-thaliana, lateral root development, length cdna microarray, 03 medical and health sciences, Stress, Physiological, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 10211 Zurich-Basel Plant Science Center, education, 030304 developmental biology, Abiotic stress, business.industry, fungi, brassica-napus, Cell Biology, 15. Life on land, biology.organism_classification, brassinosteroid signal-transduction, gene-expression, Biotechnology, Agronomy, improves drought, molecular interaction database, 13. Climate action, Protein Biosynthesis, business, Protein Kinases, water-limited conditions, Function (biology), 010606 plant biology & botany
Abstract

International audience; Global climate change and a growing population require tackling the reduction in arable land and improving biomass production and seed yield per area under varying conditions. One of these conditions is suboptimal water availability. Here, we review some of the classical approaches to dealing with plant response to drought stress and we evaluate how research on RECEPTOR-LIKE KINASES (RLKs) can contribute to improving plant performance under drought stress. RLKs are considered as key regulators of plant architecture and growth behavior, but they also function in defense and stress responses. The available literature and analyses of available transcript profiling data indeed suggest that RLKs can play an important role in optimizing plant responses to drought stress. In addition, RLK pathways are ideal targets for nontransgenic approaches, such as synthetic molecules, providing a novel strategy to manipulate their activity and supporting translational studies from model species, such as Arabidopsis thaliana, to economically useful crops.

Published
2012

26. The genome of the vervet ( Chlorocebus aethiops sabaeus )

Author

Nicoletta Archidiacono, Jennifer F. Hughes, George M. Weinstock, Yoon Jung, Christopher A. Schmitt, Angela Noll, Nelson B. Freimer, Matthew J. Jorgensen, Jennifer J. Tuscher, Nam Tran, Jason M. Brenchley, David H. O’Connor, Matthew W. Hahn, Eugene Redmond, Alex Nisbett, Roland Zahn, Hannes Svardal, Gary P. Schroth, Raquel García-Pérez, Magnus Nordborg, Nikoleta Juretic, Michael J. Montague, Gregg W.C. Thomas, Michel M. Dione, Julie A. Karl, Anna J. Jasinska, Wesley C. Warren, Jay R. Kaplan, Richard K. Wilson, Patrick Minx, Bronwen Aken, Mariano Rocchi, Colby Chiang, Françoise Thibaud-Nissen, Jessica Wasserscheid, Vasily Ramensky, Oi Wa Choi, Gennady Churakov, Roscoe Stanyon, Yu S. Huang, David Webb, Brian J. Raney, Jörn E. Schmitz, Milinn Kremitzki, Beatrice Jacquelin, Michaela Müller-Trutwin, Juergen Schmitz, Rishi Nag, Tomas Marques-Bonet, LaDeana W. Hillier, Martin Antonio, Tina Graves, Trudy R. Turner, Kim Kyung, Ken Dewar, Chad Tomlinson, Roger W. Wiseman, Oronzo Capozzi, The McDonnell Genome Institute (MGI), Washington University in Saint Louis (WUSTL), Semel Institute for Neuroscience and Human Behavior [Los Angeles, Ca], University of California [Los Angeles] (UCLA), University of California-University of California, Institute of Bioorganic Chemistry [Poznań], Polska Akademia Nauk = Polish Academy of Sciences (PAN), Institució Catalana de Recerca i Estudis Avançats (ICREA), Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), University of Bari Aldo Moro (UNIBA), Whitehead Institute, Massachusetts Institute of Technology (MIT), McGill University = Université McGill [Montréal, Canada], University of Wisconsin - Milwaukee, University of the Free State [South Africa], University of Wisconsin-Madison, Beth Israel Deaconess Medical Center [Boston] (BIDMC), Harvard Medical School [Boston] (HMS), Crucell Holland B.V, St. Kitts Biomedical Research Foundation, Régulation des Infections Rétrovirales, Institut Pasteur [Paris], National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Medical Research Council Unit The Gambia (MRC), Illumina Incorporated [San Diego, CA, USA], Wake Forest School of Medicine [Winston-Salem], Wake Forest Baptist Medical Center, Indiana University [Bloomington], Indiana University System, University of California [Santa Cruz] (UCSC), University of California, European Molecular Biology Laboratory [Hinxton], Institute of Experimental Pathology (ZMBE), Westfälische Wilhelms-Universität Münster (WWU), Institute for Evolution and Biodiversity (IEB), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), National Center for Biotechnology Information (NCBI), The Jackson Laboratory [Bar Harbor] (JAX), Funding to R.K.W. was provided by NIH-NHGRI grant 5U54HG00307907. Support for the Vervet Research Colony was provided by NIH grant RR019963/OD010965 to J.R.K. Funding to N.B.F. was provided by NIH grants R01RR016300 and R01OD010980. The French National Agency for Research on AIDS and Viral Hepatitis (ANRS) provided funding to M.C.M.-T. Funding to M.R. and R.S. was provided by the Ministero della Universita’ e della Ricerca. Funding to K.D. was provided by Genome Canada and Genome Quebec. B.A. and R.N. acknowledge support from the Wellcome Trust (grant number WT095908) and the European Molecular Biology Laboratory., We thank the following organizations for providing sampling permits and permissions: Ethiopian Wildlife Conservation Authority, Zambia Wildlife Authority, Wildlife Division, Forestry Commission, Republic of Ghana, and Gambia Department of Parks and Wildlife Management. We thank Dr. James L. Blanchard and Dr. Ivona Pandrea for vervet samples used to characterize MHC. We thank Josh McMichael and Josh Peck for figure assistance. We thank Joanne Nelson and Barbara Gillam for data submission. We thank the members of the library production group led by Catrina Fronick and sequencing led by Matt Cordes. We also thank the Medical Research Council Unit (MRC), The Gambia for their assistance, as well as all the veterinarians who worked with us to safely obtain samples., National Institutes of Health (US), National Human Genome Research Institute (US), Agence Nationale de Recherches sur le SIDA et les Hépatites Virales (France), Agence Nationale de la Recherche (France), Ministero dell'Istruzione, dell'Università e della Ricerca, Genome Canada, EMBO, Wellcome Trust, University of California (UC)-University of California (UC), Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), University of the Free State [South Africa] (UFS), Institut Pasteur [Paris] (IP), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), and Università degli Studi di Firenze = University of Florence (UniFI)

Subjects
animal diseases, [SDV]Life Sciences [q-bio], Chlorocebus aethiops, Cercopithecus aethiops, Medical and Health Sciences, Major Histocompatibility Complex, MESH: Animals, MESH: Genetic Variation, MESH: Phylogeny, Genetics (clinical), Phylogeny, MESH: Evolution, Molecular, Gene Rearrangement, education.field_of_study, Cercopithecini, Genome, biology, MESH: Genomics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], MESH: Karyotype, Genomics, Biological Sciences, 3. Good health, Rhesus macaque, Phylogeography, MESH: Phylogeography, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDE]Environmental Sciences, Complete Genome assembly, primates, cercopithecini, Infection, Biotechnology, MESH: Computational Biology, Resource, Evolution, Bioinformatics, MESH: Gene Rearrangement, Population, Karyotype, Simis, Old World monkey, MESH: Molecular Sequence Annotation, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Chromosome Painting, Evolution, Molecular, MESH: Major Histocompatibility Complex, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], parasitic diseases, Genetics, Animals, MESH: Genome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, education, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genètica animal, MESH: Chromosome Painting, Human Genome, Molecular, Computational Biology, Genetic Variation, Molecular Sequence Annotation, Gene rearrangement, biology.organism_classification, MESH: Cercopithecus aethiops, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Evolutionary biology, African Green Monkey
Abstract

Warren, Wesley C. et al., We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), for which it is the most abundant natural host species, and of a wide range of health-related phenotypes assessed in Caribbean vervets (C. a. sabaeus), whose numbers have expanded dramatically since Europeans introduced small numbers of their ancestors from West Africa during the colonial era. We use the reference to characterize the genomic relationship between vervets and other primates, the intra-generic phylogeny of vervet subspecies, and genome-wide structural variations of a pedigreed C. a. sabaeus population. Through comparative analyses with human and rhesus macaque, we characterize at high resolution the unique chromosomal fission events that differentiate the vervets and their close relatives from most other catarrhine primates, in whom karyotype is highly conserved. We also provide a summary of transposable elements and contrast these with the rhesus macaque and human. Analysis of sequenced genomes representing each of the main vervet subspecies supports previously hypothesized relationships between these populations, which range across most of sub-Saharan Africa, while uncovering high levels of genetic diversity within each. Sequence-based analyses of major histocompatibility complex (MHC) polymorphisms reveal extremely low diversity in Caribbean C. a. sabaeus vervets, compared to vervets from putatively ancestral West African regions. In the C. a. sabaeus research population, we discover the first structural variations that are, in some cases, predicted to have a deleterious effect; future studies will determine the phenotypic impact of these variations., Funding to R.K.W. was provided by NIH-NHGRI grant 5U54HG00307907. Support for the Vervet Research Colony was provided by NIH grant RR019963/OD010965 to J.R.K. Funding to N.B.F. was provided by NIH grants R01RR016300 and R01OD010980. The French National Agency for Research on AIDS and Viral Hepatitis (ANRS) provided funding to M.C.M.-T. Funding to M.R. and R.S. was provided by the Ministero della Universita’ e della Ricerca. Funding to K.D. was provided by Genome Canada and Genome Quebec. B.A. and R.N. acknowledge support from the Wellcome Trust (grant number WT095908) and the European Molecular Biology Laboratory.

Published
2015

27. GWAPP: a web application for genome-wide association mapping in Arabidopsis

Author

Magnus Nordborg, Dazhe Meng, Yu S. Huang, Bjarni J. Vilhjálmsson, Matthew W. Horton, Petar Forai, Ümit Seren, Quan Long, Vincent Segura, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Molecular and Computational Biology, University of Southern California (USC), Department of Ecology and Evolution [Chicago], University of Chicago, Center for Neurobehavioral Genetics, Semel Institute, University of California, Center for Neurobehavioral Genetics, Semel Institute, Unité de recherche Amélioration, Génétique et Physiologie Forestières (UAGPF), Institut National de la Recherche Agronomique (INRA), and Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF)

Subjects
0106 biological sciences, analyse de données, Linkage disequilibrium, cartographie génomique, genome-wide, association study, web application, linear mixed model, data analysis, association mapping, Arabidopsis, modèle linéaire mixte, Genome-wide association study, Plant Science, Computational biology, polymorphisme, 01 natural sciences, Linkage Disequilibrium, 03 medical and health sciences, User-Computer Interface, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, application web, Large-Scale Biology Article, Association mapping, Genome size, 030304 developmental biology, Genetic association, Genetics, 0303 health sciences, Internet, Vegetal Biology, biology, génome, arabidopsis thaliana, Cell Biology, Replicate, biology.organism_classification, étude d'association, Biologie végétale, Software, 010606 plant biology & botany, Genome-Wide Association Study
Abstract

Arabidopsis thaliana is an important model organism for understanding the genetics and molecular biology of plants. Its highly selfing nature, small size, short generation time, small genome size, and wide geographic distribution make it an ideal model organism for understanding natural variation. Genome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in A. thaliana. Previously genotyped accessions (natural inbred lines) can be grown in replicate under different conditions and phenotyped for different traits. These important features greatly simplify association mapping of traits and allow for systematic dissection of the genetics of natural variation by the entire A. thaliana community. To facilitate this, we present GWAPP, an interactive Web-based application for conducting GWAS in A. thaliana. Using an efficient implementation of a linear mixed model, traits measured for a subset of 1386 publicly available ecotypes can be uploaded and mapped with a mixed model and other methods in just a couple of minutes. GWAPP features an extensive, interactive, and user-friendly interface that includes interactive Manhattan plots and linkage disequilibrium plots. It also facilitates exploratory data analysis by implementing features such as the inclusion of candidate polymorphisms in the model as cofactors.

Published
2013

28. The Capsella rubella genome and the genomic consequences of rapid mating system evolution

Author

Stephen I. Wright, Daniel Koenig, Richard M. Clark, Mathieu Blanchette, Wei Wang, Hadi Quesneville, Yaniv Brandvain, Tanja Slotte, Terezie Mandáková, Jarrod Chapman, Joshua G. Steffen, L. Killian Newman, Lisa M. Smith, Kim A. Steige, Martin A. Lysak, Shohei Takuno, Adrian E. Platts, Peter Andolfatto, Detlef Weigel, Jeremy Schmutz, Shengqiang Shu, Emilio Vello, Brandon S. Gaut, Jerry Jenkins, Florian Maumus, Tina T. Hu, Stefan R. Henz, Graham Coop, Magnus Nordborg, Khaled M. Hazzouri, Ya-Long Guo, Jane Grimwood, Daniel S. Rokhsar, Juan S. Escobar, J. Arvid Ågren, Simon E. Prochnik, Department of Ecology and Evolutionary Biology, University of Toronto, Uppsala University, New York University [Abu Dhabi], NYU System (NYU), Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Chinese Academy of Sciences (CAS), Department of Evolutionary Biology, Department of Biology, Northern Arizona University [Flagstaff], Masaryk University [Brno] (MUNI), Utah State University (USU), Colby-Sawyer College, Partenaires INRAE, University of California, Department of Plant Sciences, University of California [Davis] (UC Davis), University of California-University of California, Department of Evolution and Ecology, Princeton University, McGill University = Université McGill [Montréal, Canada], Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Hudson Alpha Institute for Biotechnology, Joint Genome Institute (JGI), U.S. Department of Energy, University of California [Berkeley], and Centre for the Analysis of Genome Evolution and Function

Subjects
0106 biological sciences, Time Factors, [SDV]Life Sciences [q-bio], ved/biology.organism_classification_rank.species, Molecular Sequence Data, Arabidopsis, Outcrossing, Self-Fertilization, Genes, Plant, 01 natural sciences, Rubella, Genome, Evolution, Molecular, 03 medical and health sciences, Genetics, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Capsella, Pollination, Gene, 030304 developmental biology, genomic consequences, 0303 health sciences, biology, ved/biology, Selfing, Sequence Analysis, DNA, medicine.disease, biology.organism_classification, Mating system, Capsella rubella genome, mating systelm evolution, Fertilization, Capsella rubella, Genome, Plant, 010606 plant biology & botany
Abstract

International audience; The shift from outcrossing to selfing is common in flowering plants, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible

Published
2013

29. Recent methodological advances in GWAS: multi‐locus and multi‐trait mixed‐models

Author

Segura, Vincent, Vilhjálmsson, Bjarni J., Korte, Arthur, Platt, Alexander, Long, Quan, Nordborg, Magnus, Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut National de la Recherche Agronomique (INRA), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Department of Molecular and Computational Biology, University of Southern California (USC), and European Project: 211868

Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Abstract

absent

Published
2012

30. Dissecting the genetic basis of primary seed dormancy in arabidopsis thaliana

Author

Kerdaffrec, Envel, Segura, Vincent, Vilhjálmsson, Bjarni J., FILIAULT, DANIELE, Nordborg, Magnus, Gregor Mendel Institute, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut National de la Recherche Agronomique (INRA), Department of Epidemiology, The Netherlands Cancer Institute, Gregor Mendel Institute. AUT., and ProdInra, Migration

Subjects
marker, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, trait, phenotype, correlation, genotype, SNP, interaction, [SDV.BIO] Life Sciences [q-bio]/Biotechnology
Abstract

Seed dormancy is likely to be an important adaptive trait as it determines the right timing of seed germination. Even if several QTLs (Quantitative Trait Locus) have been identified in previous studies, it remains difficult to fully understand the genetic basis of natural variation for this trait in A. thaliana. We have found great variation for primary seed dormancy in a set of 300 Swedish accessions and we observed a strong correlation between this trait and latitude and climatic variables such as temperature and precipitation. All northern accessions seem to be non dormant whereas most of those from the south exhibit a strong primary seed dormancy. GWAS (Genome Wide Association Studies) for primary seed dormancy on a subset of 163 accessions revealed a complex 50-kilobase region encompassing the well-known gene DOG1 (Delay Of Germination 1) and at least 3 other interesting candidate genes. Although DOG1 has been reported to be one of the major seed dormancy genes, neither its function nor the causal polymorphism underlying variation in seed dormancy is known. We were able to narrow down the region of interest and we identified at least 2 candidate SNPs (Single Nucleotide Polymorphism) in the DOG1 cis regulatory region. Based on these findings, we looked at DOG1 haplotype structure and we found at least 17 haplogroups showing strong correlation with primary seed dormancy levels. Moreover, the presence of several haplotypes leading to the same dormancy phenotypes provides support for the idea of allelic heterogeneity, which could explain the complex signature of the DOG1 locus that we observed in our initial GWAS. We are currently working on the functional validation of these results.

Published
2012

31. Dissecting genetic and environmental correlation of life history traits in arabidopsis thaliana

Author

Korte, Arthur, Vilhjálmsson, Bjarni J., Segura, Vincent, Fournier-Level, Alexandre, Wilczek, Amity, Schmitt, Johanna, Nordborg, Magnus, Gregor Mendel Institute, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Department of Epidemiology, The Netherlands Cancer Institute, Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut National de la Recherche Agronomique (INRA), Department of Ecology and Evolutionary Biology, Brown University, and Gregor Mendel Institute. AUT.

Subjects
modèle mixte, marker, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, trait, phenotype, génome, genotype, arabidopsis thaliana, SNP, interaction, étude d'association pangénomique, Biotechnologies, génétique d'association, correlation, genome wide association study (GWAS)
Abstract

Due to decreasing costs of sequencing and genotyping, genome-wide association studies (GWAS) are becoming a standard approach for studying the genetics of natural variation. A major problem in such studies is the complicated dependencestructure of the data. Mixed models have emerged as a general and flexible approach for dealing with this problem. Here we extend this approach to handle correlated phenotypes by deriving a fully parameterized multi-trait mixed model (MTMM) that considers simultaneously both the within- and between-trait variance components for multiple traits. Phenotypic correlation can be due to either a common genetic architecture (pleiotropy) or to a common environmental effect. Dissecting these different causes is of interest not only because of the importance of understanding pleiotropy, but also because we may expect increased power compared to marginal analyses. To illustrate the utility of the MTMM for traits that are correlated, we reanalyzed data obtained for a set of geographically diverse ecotypes, which were grown in replicated common garden experiments in four European field sites. This data have been used successfully before to access the genetic basis for local adaptation and contain both: data for multiple phenotypes measured in the same environment, and measurements of the same phenotypes in different environments. Here we show how the genetic and environmental contribution to a specific trait can be assessed through the use of MTMM. Additionally we report newly associated markers improving our global understanding of both genetic and environmental variation on life-history traits.

Published
2012

32. Stress-induced GSK3 regulates the redox stress response by phosphorylating glucose-6-phosphate dehydrogenase in Arabidopsis

Author

Tim Clausen, Julia Krasensky, Elena Petutschnig, Yves Gibon, Silvia Dal Santo, Stefan Kempa, Alexander Heuck, Hansjörg Stampfl, Claudia Jonak, Wilfried Rozhon, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Research Institute of Molecular Pathology (IMP), and Jonak, Claudia

Subjects
0106 biological sciences, glycogène, stress salin, réponse à un stress, Plant Science, Biology, medicine.disease_cause, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, physiologie végétale, Cellular stress response, Arabidopsis, medicine, Glucose-6-phosphate dehydrogenase, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Glycogen synthase, métabolisme, biologie de la plante, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Reactive oxygen species, Vegetal Biology, arabidopsis thaliana, stress oxydatif, Cell Biology, biology.organism_classification, chemistry, Biochemistry, biology.protein, Signal transduction, Oxidative stress, Biologie végétale, 010606 plant biology & botany
Abstract

L'article original est publié par The American Society of Plant Biologists; International audience; Diverse stresses such as high salt conditions cause an increase in reactive oxygen species (ROS), necessitating a redox stress response. However, little is known about the signaling pathways that regulate the antioxidant system to counteract oxidative stress. Here, we show that a Glycogen Synthase Kinase3 from Arabidopsis thaliana (ASK alpha) regulates stress tolerance by activating Glc-6-phosphate dehydrogenase (G6PD), which is essential for maintaining the cellular redox balance. Loss of stress-activated ASK alpha leads to reduced G6PD activity, elevated levels of ROS, and enhanced sensitivity to salt stress. Conversely, plants overexpressing ASK alpha have increased G6PD activity and low levels of ROS in response to stress and are more tolerant to salt stress. ASK alpha stimulates the activity of a specific cytosolic G6PD isoform by phosphorylating the evolutionarily conserved Thr-467, which is implicated in cosubstrate binding. Our results reveal a novel mechanism of G6PD adaptive regulation that is critical for the cellular stress response.

Published
2012

33. A mixed-model approach for genome-wide association studies of correlated traits in structured populations

Author

Quan Long, Alexander Platt, Arthur Korte, Bjarni J. Vilhjálmsson, Magnus Nordborg, Vincent Segura, Austrian Academy of Sciences (OeAW), Gregor Mendel Institute of Molecular Plant Biology (GMI), Department of Molecular and Computational Biology, University of Southern California (USC), Unité de recherche Amélioration, Génétique et Physiologie Forestières (UAGPF), Institut National de la Recherche Agronomique (INRA), Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Korte, Arthur, Vilhjálmsson, Bjarni J, and Segura, Vincent

Subjects
0106 biological sciences, Mixed model, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Arabidopsis, Genome-wide association study, Flowers, Computational biology, Polymorphism, Single Nucleotide, 01 natural sciences, Article, Cohort Studies, 03 medical and health sciences, Genetics, corrélation entre les caractères, Cluster Analysis, Humans, Arabidopsis thaliana, Computer Simulation, Finland, 030304 developmental biology, Genetic association, modèle mixte, 0303 health sciences, Models, Genetic, biology, génome, plasticité, fungi, food and beverages, Lipid Metabolism, biology.organism_classification, Lipids, Phenotype, Genetics, Population, Gene-Environment Interaction, étude d'association, Genome, Plant, Genome-Wide Association Study, 010606 plant biology & botany
Abstract

Genome-wide association studies (GWAS) are a standard approach for studying the genetics of natural variation. A major concern in GWAS is the need to account for the complicated dependence structure of the data, both between loci as well as between individuals. Mixed models have emerged as a general and flexible approach for correcting for population structure in GWAS. Here, we extend this linear mixed-model approach to carry out GWAS of correlated phenotypes, deriving a fully parameterized multi-trait mixed model (MTMM) that considers both the within-trait and between-trait variance components simultaneously for multiple traits. We apply this to data from a human cohort for correlated blood lipid traits from the Northern Finland Birth Cohort 1966 and show greatly increased power to detect pleiotropic loci that affect more than one blood lipid trait. We also apply this approach to an Arabidopsis thaliana data set for flowering measurements in two different locations, identifying loci whose effect depends on the environment.

Published
2012

34. The Balance between the MIR164A and CUC2 Genes Controls Leaf Margin Serration in Arabidopsis

Author

Hasson, Alice, Pulido, Amada, Vialette-Guiraud, Aurélie, Hay, Angela, Johansen, Ida Elisabeth, Tsiantis, Miltos, Raman, Smita, Greb, Thomas, Theres, Klaus, Nikovics, Krisztina, Blein, Thomas, Peaucelle, Alexis, Ishida, Tetsuya, Morin, Halima, Aida, Mitsuhiro, Laufs, Patrick, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Department of Plant Biochemistry, Cell and Molecular Biology, Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Max Planck Institute for Plant Breeding Research (MPIPZ), Department of Plant and Environmental Sciences, department of Plant, Department of Plant Sciences, University of Oxford [Oxford], Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Institut des sciences du végétal (ISV), Centre National de la Recherche Scientifique (CNRS), Grad Sch Biol Sci, Nara Institute of Science and Technology, École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Mutant, Arabidopsis, Gene Expression, Plant Science, Flowers, Genes, Plant, 01 natural sciences, Models, Biological, Conserved sequence, 03 medical and health sciences, Gene expression, Botany, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Primordium, Research Articles, Alleles, Conserved Sequence, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, biology, Arabidopsis Proteins, fungi, Genetic Complementation Test, Wild type, food and beverages, Cell Biology, Meristem, biology.organism_classification, Plants, Genetically Modified, Cell biology, Plant Leaves, Serration, MicroRNAs, Mutation, Nucleic Acid Conformation, 010606 plant biology & botany
Abstract

CUP-SHAPED COTYLEDON1 (CUC1), CUC2, and CUC3 define the boundary domain around organs in the Arabidopsis thaliana meristem. CUC1 and CUC2 transcripts are targeted by a microRNA (miRNA), miR164, encoded by MIR164A, B, and C. We show that each MIR164 is transcribed to generate a large population of primary miRNAs of variable size with a locally conserved secondary structure around the pre-miRNA. We identified mutations in the MIR164A gene that deepen serration of the leaf margin. By contrast, leaves of plants overexpressing miR164 have smooth margins. Enhanced leaf serration was observed following the expression of an miR164-resistant CUC2 but not of an miR164-resistant CUC1. Furthermore, CUC2 inactivation abolished serration in mir164a mutants and the wild type, whereas CUC1 inactivation did not. Thus, CUC2 specifically controls leaf margin development. CUC2 and MIR164A are transcribed in overlapping domains at the margins of young leaf primordia, with transcription gradually restricted to the sinus, where the leaf margins become serrated. We suggest that leaf margin development is controlled by a two-step process in Arabidopsis. The pattern of serration is determined first, independently of CUC2 and miR164. The balance between coexpressed CUC2 and MIR164A then determines the extent of serration.

Published
2006

35. The Arabidopsis thaliana MND1 homologue plays a key role in meiotic homologous pairing, synapsis and recombination

Author

Peter Schlögelhofer, Andrea Pedrosa-Harand, Robert Sablowski, Rapheal Mercier, Tanja Siwiec, Julien Vignard, Claudia Kerzendorfer, Sylvie Jolivet, Svetlana Akimcheva, Susan J. Armstrong, Dieter Schweizer, Unité de recherche Génétique et amélioration des plantes (GAP), Institut National de la Recherche Agronomique (INRA), University of Vienna [Vienna], Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Department of Cell and Developmental Biology, John Innes Centre [Norwich], School of Biosciences, and University of Birmingham [Birmingham]

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Arabidopsis, Biology, 01 natural sciences, Genetic recombination, GENE atMND1, Chromosomal crossover, 03 medical and health sciences, Meiosis, Homologous chromosome, 030304 developmental biology, Recombination, Genetic, Genetics, 0303 health sciences, Arabidopsis Proteins, fungi, Synapsis, ARABIDOPSIS THALIANA, Cell Biology, AMELIORATION DES PLANTES, BIOLOGIE MOLECULAIRE, GENETIQUE, Establishment of sister chromatid cohesion, Chromosome Pairing, Synaptonemal complex, MEIOSE, RECOMBINAISON HOMOLOGUE, Mutation, Homologous recombination, REPRODUCTION SEXUEE, DNA Damage, 010606 plant biology & botany
Abstract

International audience; Mnd1 has recently been identified in yeast as a key player in meiotic recombination. Here we describe the identification and functional characterisation of the Arabidopsis homologue, AtMND1, which is essential for male and female meiosis and thus for plant fertility. Although axial elements are formed normally, sister chromatid cohesion is established and recombination initiation appears to be unaffected in mutant plants, chromosomes do not synapse. During meiotic progression, a mass of entangled chromosomes, interconnected by chromatin bridges, and severe chromosome fragmentation are observed. These defects depend on the presence of SPO11-1, a protein that initiates recombination by catalysing DNA double-strand break (DSB) formation. Furthermore, we demonstrate that the AtMND1 protein interacts with AHP2, the Arabidopsis protein closely related to budding yeast Hop2. These data demonstrate that AtMND1 plays a key role in homologous synapsis and in DSB repair during meiotic recombination.

Published
2006

36. Fifteen compelling open questions in plant cell biology

Author

Ram Dixit, Maria J. Harrison, Gohta Goshima, Adrienne H. K. Roeder, David W. Ehrhardt, Christine Faulkner, Jeff J. Doyle, Jeremy E. Coate, Marisa S. Otegui, Arezki Boudaoud, Keiko Sugimoto, Yan Zhang, Liam Dolan, Charlotte Kirchhelle, Carlos D. Messina, Heather M Meyer, Olivier Hamant, Charles T. Anderson, Cornell University [New York], University of Wisconsin-Madison, Washington University in Saint Louis (WUSTL), Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB, UK, Sugashima Marine Biological Laboratory, Nagoya University, Marine Biological Laboratory, Woods Hole, Massachusetts, USA, Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Department of Plant Biology [Carnegie] (DPB), Carnegie Institution for Science, Laboratoire d'hydrodynamique (LadHyX), and École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Cell type, AcademicSubjects/SCI01280, Somatic cell, [SDV]Life Sciences [q-bio], Reviews, Plant Science, Plasmodesma, Vacuole, Biology, 01 natural sciences, 03 medical and health sciences, Organelle, Cortical microtubule cytoskeleton, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, AcademicSubjects/SCI01270, AcademicSubjects/SCI02288, AcademicSubjects/SCI02287, fungi, AcademicSubjects/SCI02286, food and beverages, Cell Biology, Cell biology, Focus on Cell Biology, Retrograde signaling, 010606 plant biology & botany, Cell division site
Abstract

As scientists, we are at least as excited about the open questions—the things we do not know—as the discoveries. Here, we asked 15 experts to describe the most compelling open questions in plant cell biology. These are their questions: How are organelle identity, domains, and boundaries maintained under the continuous flux of vesicle trafficking and membrane remodeling? Is the plant cortical microtubule cytoskeleton a mechanosensory apparatus? How are the cellular pathways of cell wall synthesis, assembly, modification, and integrity sensing linked in plants? Why do plasmodesmata open and close? Is there retrograde signaling from vacuoles to the nucleus? How do root cells accommodate fungal endosymbionts? What is the role of cell edges in plant morphogenesis? How is the cell division site determined? What are the emergent effects of polyploidy on the biology of the cell, and how are any such “rules” conditioned by cell type? Can mechanical forces trigger new cell fates in plants? How does a single differentiated somatic cell reprogram and gain pluripotency? How does polarity develop de-novo in isolated plant cells? What is the spectrum of cellular functions for membraneless organelles and intrinsically disordered proteins? How do plants deal with internal noise? How does order emerge in cells and propagate to organs and organisms from complex dynamical processes? We hope you find the discussions of these questions thought provoking and inspiring., We asked 15 experts to address what they consider to be the most compelling open questions in plant cell biology and these are their questions.

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37. Chemical Inhibition of a Subset of Arabidopsis thaliana GSK3-like Kinases Activates Brassinosteroid Signaling

Author

Long Nguyen, Dominique Audenaert, Eugenia Russinova, Juliane Mayerhofer, Gerrit T.S. Beemster, Tinneke Denayer, Dirk Inzé, Claudia Jonak, Grégory Vert, Silvie Coutuer, Wilfried Rozhon, Tom Beeckman, Kris Vleminckx, Isabelle Vanhoutte, Joanne Chory, Bert De Rybel, Leentje Jansen, Frank Peelman, Department of Systems Biology, VIB, Universiteit Gent [Ghent], Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Department of Medical Protein Research, Department of Biochemistry, Ghent University [Belgium] (UGENT)-Faculty of Medicine and Health Sciences, Department of Molecular Biomedical Research, Ghent University [Belgium] (UGENT), Department of Molecular Biology, Compound Screening Facility, Department of Biology, University of Antwerp (UA), Plant Biology Laboratory and Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Universiteit Gent = Ghent University [Belgium] (UGENT), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Universiteit Gent = Ghent University [Belgium] (UGENT)-Faculty of Medicine and Health Sciences

Subjects
0106 biological sciences, Clinical Biochemistry, Regulator, Aminopyridines, 01 natural sciences, Biochemistry, GSK3, Glycogen Synthase Kinase 3, chemistry.chemical_compound, GSK-3, Arabidopsis, Drug Discovery, Protein Isoforms, Brassinosteroid, Phosphorylation, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, biology, Kinase, Nuclear Proteins, General Medicine, ARABIDOPSIS, Cell biology, DNA-Binding Proteins, Molecular Medicine, Signal transduction, Signal Transduction, Molecular Sequence Data, Article, 03 medical and health sciences, Steroids, Heterocyclic, Brassinosteroids, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Amino Acid Sequence, Protein kinase A, Biology, Molecular Biology, 030304 developmental biology, Pharmacology, Sequence Homology, Amino Acid, Arabidopsis Proteins, ACL, Succinates, biology.organism_classification, CHEMBIO, chemistry, Protein Kinases, Cholestanols, BRASSINOSTEROID SIGNALING, 010606 plant biology & botany
Abstract

International audience; Glycogen synthase kinase 3 (GSK3) is a key regulator in signaling pathways in both animals and plants. Three Arabidopsis thaliana GSK3s are shown to be related to brassinosteroid (BR) signaling. In a phenotype-based compound screen we identified bikinin, a small molecule that activates BR signaling downstream of the BR receptor. Bikinin directly binds the GSK3 BIN2 and acts as an ATP competitor. Furthermore, bikinin inhibits the activity of six other Arabidopsis GSK3s. Genome-wide transcript analyses demonstrate that simultaneous inhibition of seven GSK3s is sufficient to activate BR responses. Our data suggest that GSK3 inhibition is the sole activation mode of BR signaling and argues against GSK3-independent BR responses in Arabidopsis. The opportunity to generate multiple and conditional knockouts in key regulators in the BR signaling pathway by bikinin represents a useful tool to further unravel regulatory mechanisms.

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38. Genome sequencing reveals the origin of the allotetraploid Arabidopsis suecica

Author

Elisa Prat, Magnus Nordborg, Viktoria Nizhynska, Torbjörn Säll, Viktor Voronin, William Marande, Takashi Tsuchimatsu, Robin Burns, Svante Holm, Samson Simon, Vincent Castric, Polina Yu. Novikova, Olga M. Fedorenko, Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, UMR 8198 - Evolution, Ecologie et Paléontologie, Université de Lille, Institute of Biology, University of Iceland [Reykjavik], Faculty of Science, Technology and Media, Department of Natural Sciences, Mid Sweden University, Department of Biology, Northern Arizona University [Flagstaff], Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), European Research Council (ERC) under the European Union 648321, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Gregor Mendel Institute (GMI) - Vienna Biocenter (VBC), Austrian Academy of Sciences (OeAW), Gregor Mendel Institute of Molecular Plant Biology (GMI), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and Nordborg, Magnus

Subjects
0301 basic medicine, Arabidopsis thaliana, Arabidopsis, polymorphisme, polymorphism, shared polymorphism, Biologiska vetenskaper, hybridization, polyploidy, ComputingMilieux_MISCELLANEOUS, Phylogeny, Genetics, Vegetal Biology, Genome, asexualite, Chromosome Mapping, self fertilization, Arabidopsis suecica, Biological Sciences, séquençage du génome, Genome, Plant, Genetic Speciation, Locus (genetics), Self-Fertilization, Biology, Asexuality, Arabidopsis arenosa, Polyploidy, 03 medical and health sciences, Polyploid, arenosa, speciation, polyploïdie, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Allele, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Discoveries, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Base Sequence, Selfing, cytotype, Genetic Variation, Sequence Analysis, DNA, biology.organism_classification, Tetraploidy, 030104 developmental biology, hybridation, Biologie végétale, autofécondation
Abstract

Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual—a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-of-function allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous.

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39. Crosstalk between H2A variant-specific modifications impacts vital cell functions

Author

Frédéric Berger, Bingkun Lei, Zdravko Lorkovic, Sigurd Braun, Pierre Bourguet, Olivier Mathieu, Karl Mechtler, Matías Capella, Anna Schmuecker, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Ludwig-Maximilians-Universität München (LMU), Génétique, Reproduction et Développement (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), and Mathieu, Olivier

Subjects
Cancer Research, Chromosomal Proteins, Non-Histone, Cell, Arabidopsis, Cell Culture Techniques, Yeast and Fungal Models, [SDV.GEN] Life Sciences [q-bio]/Genetics, QH426-470, Biochemistry, Histones, Schizosaccharomyces Pombe, 0302 clinical medicine, Gene Expression Regulation, Plant, Heterochromatin, Protein Isoforms, Transgenes, Cell Cycle and Cell Division, Phosphorylation, Post-Translational Modification, Genetics (clinical), 0303 health sciences, biology, Kinase, Chemistry, Cell Cycle, Eukaryota, Plants, Plants, Genetically Modified, Cyclin-Dependent Kinases, Chromatin, Precipitation Techniques, Cell biology, Nucleic acids, Crosstalk (biology), medicine.anatomical_structure, Histone, Experimental Organism Systems, Cell Processes, embryonic structures, Research Article, animal structures, Immunoprecipitation, DNA damage, Arabidopsis Thaliana, Brassica, Research and Analysis Methods, Evolution, Molecular, 03 medical and health sciences, Model Organisms, Plant and Algal Models, Plant Cells, Schizosaccharomyces, DNA-binding proteins, Histone H2A, medicine, Genetics, Nucleosome, Amino Acid Sequence, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, [SDV.GEN]Life Sciences [q-bio]/Genetics, Sequence Homology, Amino Acid, Arabidopsis Proteins, Organisms, Fungi, Biology and Life Sciences, Proteins, DNA, Cell Biology, biology.organism_classification, Yeast, Seedlings, Schizosaccharomyces pombe, Animal Studies, biology.protein, Schizosaccharomyces pombe Proteins, Protein Processing, Post-Translational, Sequence Alignment, 030217 neurology & neurosurgery, Function (biology)
Abstract

Selection of C-terminal motifs participated in evolution of distinct histone H2A variants. Hybrid types of variants combining motifs from distinct H2A classes are extremely rare. This suggests that the proximity between the motif cases interferes with their function. We studied this question in flowering plants that evolved sporadically a hybrid H2A variant combining the SQ motif of H2A.X that participates in the DNA damage response with the KSPK motif of H2A.W that stabilizes heterochromatin. Our inventory of PTMs of H2A.W variants showed that in vivo the cell cycle-dependent kinase CDKA phosphorylates the KSPK motif of H2A.W but only in absence of an SQ motif. Phosphomimicry of KSPK prevented DNA damage response by the SQ motif of the hybrid H2A.W/X variant. In a synthetic yeast expressing the hybrid H2A.W/X variant, phosphorylation of KSPK prevented binding of the BRCT-domain protein Mdb1 to phosphorylated SQ and impaired response to DNA damage. Our findings illustrate that PTMs mediate interference between the function of H2A variant specific C-terminal motifs. Such interference could explain the mutual exclusion of motifs that led to evolution of H2A variants., Author summary DNA is wrapped around nucleosomes constituted by histones. Variants of histones diversified during evolution. The evolutionary path that led to selection of C-terminal motifs specific of each class of H2A variant is largely unknown. Here we show that cell cycle dependent kinases phosphorylate the KSPK motif identifying the heterochromatin-associated variant H2A.W that evolved in vascular plants. In all eukaryotes, H2A.X carries the SQ motif that is phosphorylated in response to DNA damage. Assembling both motifs in the C-terminal tail is rarely seen in hybrid H2A.W/X variants that evolved in a few plant species. Genetic manipulations in Arabidopsis show that this is possible only if phosphorylation of the KSPK motif is prevented. A synthetic strategy using yeast shows that KSPK phosphorylation interferes with the recognition of the reader of phosphorylated SQ and hampers with DNA damage response. This study proposes that interference between the function carried by C-terminal motifs led to their mutual exclusion achieving evolution of distinct classes of H2A variants.

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