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9 results on '"MESH : Models, Genetic"'

1. Trm112p Is a 15-kDa Zinc Finger Protein Essential for the Activity of Two tRNA and One Protein Methyltransferases in Yeast

Author

Léon Dirick, Bruno Lapeyre, Glenn R. Björk, Marie-Hélène Mazauric, Suresh K. Purushothaman, Centre de recherches de biochimie macromoléculaire ( CRBM ), Université Montpellier 1 ( UM1 ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -IFR122-Centre National de la Recherche Scientifique ( CNRS ), Institut de Génétique Moléculaire de Montpellier ( IGMM ), Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Institut de Génétique Moléculaire de Montpellier (IGMM), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)

Subjects
Proteomics, MESH : DNA, MESH: tRNA Methyltransferases, MESH : Saccharomyces cerevisiae, MESH : Models, Genetic, Biochemistry, MESH: Recombinant Proteins, MESH : Proteomics, MESH: Saccharomyces cerevisiae Proteins, MESH : Anticodon, RNA, Transfer, MESH : Catalysis, MESH: Models, Genetic, Zinc finger, tRNA Methyltransferases, MESH : Cell Nucleus, 0303 health sciences, MESH : Chromatin, MESH: Proteomics, 030302 biochemistry & molecular biology, MESH: DNA, Zinc Fingers, MESH : Protein Binding, Translation (biology), MESH: Saccharomyces cerevisiae, MESH : Mitosis, Chromatin, Recombinant Proteins, MESH : tRNA Methyltransferases, Transfer RNA, T arm, MESH : Mutation, Protein Binding, MESH: Cell Nucleus, TRNA modification, Saccharomyces cerevisiae Proteins, MESH: Mutation, MESH : Recombinant Proteins, Saccharomyces cerevisiae, Mitosis, MESH : RNA, Transfer, Biology, Catalysis, Chromatin remodeling, MESH: Chromatin, MESH : Saccharomyces cerevisiae Proteins, 03 medical and health sciences, Anticodon, MESH: Anticodon, MESH: Zinc Fingers, MESH: Protein Binding, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Zinc Fingers, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, 030304 developmental biology, Cell Nucleus, Models, Genetic, TRNA Methyltransferase, DNA, Cell Biology, MESH: Mitosis, MESH: Catalysis, MESH: RNA, Transfer, biology.organism_classification, Mutation, RNA
Abstract

International audience; The degenerate base at position 34 of the tRNA anticodon is the target of numerous modification enzymes. In Saccharomyces cerevisiae, five tRNAs exhibit a complex modification of uridine 34 (mcm(5)U(34) and mcm(5)s(2)U(34)), the formation of which requires at least 25 different proteins. The addition of the last methyl group is catalyzed by the methyltransferase Trm9p. Trm9p interacts with Trm112p, a 15-kDa protein with a zinc finger domain. Trm112p is essential for the activity of Trm11p, another tRNA methyltransferase, and for Mtq2p, an enzyme that methylates the translation termination factor eRF1/Sup45. Here, we report that Trm112p is required in vivo for the formation of mcm(5)U(34) and mcm(5)s(2)U(34). When produced in Escherichia coli, Trm112p forms a complex with Trm9p, which renders the latter soluble. This recombinant complex catalyzes the formation of mcm(5)U(34) on tRNA in vitro but not mcm(5)s(2)U(34). An mtq2-0 trm9-0 strain exhibits a synthetic growth defect, thus revealing the existence of an unexpected link between tRNA anticodon modification and termination of translation. Trm112p is associated with other partners involved in ribosome biogenesis and chromatin remodeling, suggesting that it has additional roles in the cell.

Published
2010

2. Adipose tissue transcriptome reflects variations between subjects with continued weight loss and subjects regaining weight 6 mo after caloric restriction independent of energy intake

Author

Adriana Márquez-Quiñones, Dominique Langin, Karine Clément, Wim H. M. Saris, Teodora Handjieva-Darlenska, Marion Combes, Ping Wang, Andreas Pfeiffer, Dimitris K. Babalis, David M. Mutch, Thomas Meinert Larsen, Susan A. Jebb, Claus Holst, Edwin C. M. Mariman, Hubert Vidal, Arne Astrup, Nathalie Viguerie, Pavla Kalouskova, Balbine Roussel, Cyrille Debard, J. Alfredo Martínez, Institut de médecine moléculaire de Rangueil (I2MR), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-IFR150-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Santé Publique et Informatique Médicale (SPIM), Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Human Health and Nutritional Sciences, University of Guelph, Régulations métaboliques, nutrition et diabètes - UM55 (RMND UM55), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Recherche Agronomique (INRA), Department of Human Biology, Maastricht University [Maastricht], Institute of Preventive Medicine, Copenhagen University Hospitals, Department of Physiology and Nutrition, Universidad de Navarra [Pamplona] (UNAV), Department of Pharmacology and Toxicology, Medical Faculty, Medical University, Obesity Management Centre, Institute of Endocrinology, Human Nutrition Research, Elsie Widdowson Laboratory, Department of Internal Medicine, University Hospital of Heraklion, Department of Clinical Nutrition, Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Department of Human Nutrition, Faculty of Life Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Centre de Recherche en Nutrition Humaine d'Ile-de-France (CRNH-IDF), Université Paris 13 (UP13)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Veille Sanitaire (INVS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut National Agronomique Paris-Grignon (INA P-G)-CETAF-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Biochimie [Purpan], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-CHU Toulouse [Toulouse]-Institut Fédératif de Biologie (IFB) - Hôpital Purpan, Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse]-CHU Toulouse [Toulouse]-Hôpital Purpan [Toulouse], CHU Toulouse [Toulouse], European Community [FP6-513946], Institut National de la Sante et de la Recherche Medicale, Region Midi-Pyrenees, Université de Toulouse (UT)-Université de Toulouse (UT)- Institut Fédératif de Recherche Bio-médicale Institution (IFR150)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Hospices Civils de Lyon (HCL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Université Paris 13 (UP13)-Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Veille Sanitaire (INVS)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut National Agronomique Paris-Grignon (INA P-G)-CETAF-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Biochimie [CHU Toulouse], Institut Fédératif de Biologie (IFB), Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Centre Hospitalier Universitaire de Toulouse (CHU Toulouse)-Pôle Biologie [CHU Toulouse], Centre Hospitalier Universitaire de Toulouse (CHU Toulouse), Simon, Marie Francoise, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées- Institut Fédératif de Recherche Bio-médicale Institution (IFR150)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de médecine moléculaire de Rangueil ( I2MR ), Université Toulouse III - Paul Sabatier ( UPS ), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-IFR150-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire de Santé Publique et Informatique Médicale ( SPIM ), Institut National de la Santé et de la Recherche Médicale ( INSERM ), Régulations métaboliques, nutrition et diabètes - UM55 ( RMND UM55 ), Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Institut National des Sciences Appliquées ( INSA ) -Hospices Civils de Lyon ( HCL ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Institut National de la Recherche Agronomique ( INRA ), Universidad de Navarra [Pamplona] ( UNAV ), Charité Universitäts Medizin Berlin, University of Copenhagen ( KU ), Centre de Recherche en Nutrition Humaine d'Ile-de-France ( CRNH-IDF ), Université Paris 13 ( UP13 ) -Institut National de la Recherche Agronomique ( INRA ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de Veille Sanitaire (INVS)-Assistance publique - Hôpitaux de Paris (AP-HP)-Conservatoire National des Arts et Métiers [CNAM] ( CNAM ) -Institut National Agronomique Paris-Grignon ( INA P-G ) -CETAF-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Charité - Universitätsmedizin Berlin / Charite - University Medicine Berlin, Université Paris 13 (UP13)-CETAF-Institut National Agronomique Paris-Grignon (INA P-G)-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Institut de Veille Sanitaire (INVS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Humane Biologie, RS: NUTRIM - R4 - Gene-environment interaction, and RS: NUTRIM - R1 - Metabolic Syndrome

Subjects
MESH: Treatment Failure, Blood Pressure, MESH: Energy Intake, Transcriptome, 0302 clinical medicine, HIGH-PROTEIN, Models, MESH: Models, Genetic, GENE-EXPRESSION, Oligonucleotide Array Sequence Analysis, MESH: Treatment Outcome, 0303 health sciences, MACRONUTRIENT, Reducing, MESH : Reverse Transcriptase Polymerase Chain Reaction, MESH: Blood Pressure, MESH: Follow-Up Studies, LOW-FAT, Gene expression profiling, 3. Good health, MESH : Oligonucleotide Array Sequence Analysis, Adipose Tissue, MESH: Adipose Tissue, medicine.medical_specialty, Diet, Reducing, LOSS MAINTENANCE, MESH : Adipose Tissue, 03 medical and health sciences, MESH: Gene Expression Profiling, MESH: Weight Loss, MESH : Treatment Failure, Genetic, Humans, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Humans, MESH : Gene Expression Profiling, MESH : Humans, MESH : Follow-Up Studies, MESH: Adult, Anthropometry, medicine.disease, Obesity, Endocrinology, MICROARRAY DATA, Energy intake, MESH: Female, Calorie, Time Factors, Medicine (miscellaneous), Adipose tissue, MESH : Models, Genetic, HUMAN OBESITY, Weight loss, MESH: Reverse Transcriptase Polymerase Chain Reaction, MESH : RNA, MESH: Obesity, MESH : Female, Treatment Failure, MESH : Diet, Reducing, 2. Zero hunger, MESH: Diet, Reducing, Nutrition and Dietetics, Reverse Transcriptase Polymerase Chain Reaction, MESH : Adult, ADIPOCYTES, Glycemic index, Treatment Outcome, MESH : Obesity, Female, medicine.symptom, Dieting, MESH : Time Factors, Adult, 030209 endocrinology & metabolism, MESH : Treatment Outcome, Biology, DiOGenes, MESH: RNA, Internal medicine, Weight Loss, medicine, MESH : Blood Pressure, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, LOSS DIETS, Models, Genetic, Gene Expression Profiling, MESH: Time Factors, MESH : Energy Intake, Diet, MESH: Oligonucleotide Array Sequence Analysis, GLYCEMIC INDEX, RNA, MESH : Weight Loss, Energy Intake, Follow-Up Studies
Abstract

Background: The mechanisms underlying body weight evolution after diet-induced weight loss are poorly understood. Objective: We aimed to identify and characterize differences in the subcutaneous adipose tissue (SAT) transcriptome of subjects with different weight changes after energy restriction-induced weight loss during 6 mo on 4 different diets. Design: After an 8-wk low-calorie diet (800 kcal/d), we randomly assigned weight-reduced obese subjects from 8 European countries to receive 4 diets that differed in protein and glycemic index content. In addition to anthropometric and plasma markers, SAT biopsies were taken at the beginning [clinical investigation day (CID) 2] and end (CID3) of the weight follow-up period. Microarray analysis was used to define SAT gene expression profiles at CID2 and CID3 in 22 women with continued weight loss (successful group) and in 22 women with weight regain (unsuccessful group) across the 4 dietary arms. Results: Differences in SAT gene expression patterns between successful and unsuccessful groups were mainly due to weight variations rather than to differences in dietary macronutrient content. An analysis of covariance with total energy intake as a covariate identified 1338 differentially expressed genes. Cellular growth and proliferation, cell death, cellular function, and maintenance were the main biological processes represented in SAT from subjects who regained weight. Mitochondrial oxidative phosphorylation was the major pattern associated with continued weight loss. Conclusions: The ability to control body weight loss independent of energy intake or diet composition is reflected in the SAT transcriptome. Although cell proliferation may be detrimental, a greater mitochondrial energy gene expression is suggested as being beneficial for weight control. This trial was registered at clinicaltrials.gov as NCT00390637. © 2010 American Society for Nutrition.

Published
2010

3. Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays

Author

Elodie Manié, Emmanuel Barillot, Marc-Henri Stern, Tatiana Popova, Dominique Stoppa-Lyonnet, Guillem Rigaill, Unité de génétique et biologie des cancers ( U830 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut Curie-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Département de Biologie des Tumeurs, INSTITUT CURIE, Mathématiques et Informatique Appliquées ( MIA-Paris ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Département de recherche translationnelle, Cancer et génôme: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, MINES ParisTech - École nationale supérieure des mines de Paris-Institut National de la Santé et de la Recherche Médicale ( INSERM ) -INSTITUT CURIE, This work is part of the 'Cancéropôle Ile-de-France-Région Ile-de-France-Hereditary Breast Cancer' program coordinated by DSL and MHS. This work also was supported by the INSERM, the Institut Curie, and its Translational Research Department. TP is supported by a grant from the Cancéropôle Ile-de-France-Région Ile-de-France. GR is supported by a grant from the Institut National du Cancer (INCa)., Unité de génétique et biologie des cancers (U830), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Curie, Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), MINES ParisTech - École nationale supérieure des mines de Paris-Institut Curie-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5), Institut Curie [Paris], Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, MINES ParisTech - 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), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Département de Recherche Translationnelle, Mines Paris - PSL (École nationale supérieure des mines de Paris), and BMC, Ed.

Subjects
Method, Loss of Heterozygosity, MESH : Models, Genetic, MESH : Genotype, [SDV.GEN] Life Sciences [q-bio]/Genetics, Allelic Imbalance, MESH : Breast Neoplasms, Genome, Loss of heterozygosity, MESH: Genotype, Automation, MESH: Ploidies, 0302 clinical medicine, Models, MESH: Automation, Genotype, MESH: Models, Genetic, MESH : Karyotyping, Genetics, 0303 health sciences, MESH: Polymorphism, Single Nucleotide, MESH: Genomics, Homozygote, MESH : Polymorphism, Single Nucleotide, Single Nucleotide, Genomics, MESH: Gene Expression Regulation, Neoplastic, SDV:GEN, Gene Expression Regulation, Neoplastic, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], 030220 oncology & carcinogenesis, MESH : Ploidies, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH: Homozygote, MESH : Gene Expression Regulation, Neoplastic, Breast Neoplasms, Biology, Polymorphism, Single Nucleotide, 03 medical and health sciences, MESH: Gene Expression Profiling, MESH : Homozygote, Genetic, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], SNP, Humans, MESH: Genome, Polymorphism, MESH : Allelic Imbalance, 030304 developmental biology, MESH: Loss of Heterozygosity, Neoplastic, [SDV.GEN]Life Sciences [q-bio]/Genetics, Ploidies, MESH: Humans, Models, Genetic, Gene Expression Profiling, MESH : Gene Expression Profiling, MESH : Genomics, MESH : Humans, MESH: Allelic Imbalance, Gene Expression Regulation, Karyotyping, SDV:BBM:GTP, Human genetics, MESH : Automation, Gene expression profiling, MESH: Karyotyping, MESH : Genome, [ SDV.GEN ] Life Sciences [q-bio]/Genetics, MESH: Breast Neoplasms, MESH : Loss of Heterozygosity
Abstract

GAP, a method for analyzing complex cancer genome profiles from SNP arrays, performs well even with poor quality data and rearranged genomes, We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Assignments were verified by DNA indexes of primary tumors and karyotypes of cell lines. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes.

Published
2009

4. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths

Author

Edouard Bingen, Olivier Clermont, Chantal Le Bouguénec, Zoé Rouy, Sophie Oztas, James R. Johnson, Anne-Marie Gilles, Erick Denamur, Marie Touchon, Olivier Tenaillon, David Vallenet, Valérie Barbe, Marie-Agnès Petit, Meriem El Karoui, Stéphane Bonacorsi, Dominique Schneider, Louis Garry, Eduardo P. C. Rocha, Alexandra Calteau, Antoine Danchin, Xavier Nassif, Ivan Matic, Vanessa Martinez-Jéhanne, Jérôme Tourret, Sophie Mangenot, Christophe Pichon, Jean Marc Ghigo, Claude Saint Ruf, Philippe Bidet, Claire Hoede, Eric Frapy, Christiane Bouchier, Simon Baeriswyl, Benoit Vacherie, Stéphane Cruveiller, Mathilde Lescat, Odile Bouvet, Carole Dossat, Claudine Médigue, Médéric Diard, Hélène Chiapello, Atelier de BioInformatique (ABI), Université Pierre et Marie Curie - Paris 6 (UPMC), Génomique évolutive des microbes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Ecologie et Evolution des Microorganismes (EEM), Université Paris 13 (UP13)-Université Paris Diderot - Paris 7 (UPD7)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-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), Génétique moléculaire, évolutive et médicale, IFR65-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris 7, Hôpital Robert Debré-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris] (IP), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Mathématique, Informatique, et Génomique, Institut National de la Recherche Agronomique (INRA), Génétique des Génomes Bactériens, Pathogénie des infections systémiques (UMR_S 570), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génétique des Biofilms, Veterans Affairs Medical Center, Department of Medecine, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Pathogénie Bactérienne des Muqueuses, Unité des Bactéries Lactiques et Pathogènes Opportunistes, Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] (LAPM), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Gagnon, Jean, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Paris Diderot - Paris 7 (UPD7)-Université Paris 13 (UP13)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Génomique (Plate-Forme), Institut Pasteur [Paris], University of Minnesota [Twin Cities], IFR65-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF), Atelier de BioInformatique ( ABI ), Université Pierre et Marie Curie - Paris 6 ( UPMC ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Ecologie et Evolution des Microorganismes ( EEM ), Université Paris 13 ( UP13 ) -Université Paris Diderot - Paris 7 ( UPD7 ) -Université Sorbonne Paris Cité ( USPC ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), IFR65-Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Hôpital Robert Debré-Université Paris Diderot - Paris 7 ( UPD7 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut National de la Recherche Agronomique ( INRA ), Pathogénie des infections systémiques ( UMR_S 570 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), University of Minnesota [Minneapolis], Laboratoire Adaptation et pathogénie des micro-organismes [Grenoble] ( LAPM ), and Université Joseph Fourier - Grenoble 1 ( UJF ) -Centre National de la Recherche Scientifique ( CNRS )

Subjects
MESH : Escherichia coli, Cancer Research, MESH : Polymorphism, Genetic, MESH : Recombination, Genetic, MESH : Models, Genetic, MESH : Models, Biological, MESH: Genome, Bacterial, Genome, MESH: Genetics, Gene flow, MESH : Genetics, MESH: Models, Genetic, MESH: Phylogeny, bioinformatique, Phylogeny, Genetics (clinical), MESH: Evolution, Molecular, Recombination, Genetic, bactérie, 2. Zero hunger, Genetics, Likelihood Functions, 0303 health sciences, Phylogenetic tree, MESH: Escherichia coli, MESH: Genomics, Genomics, Genome project, Evolutionary Biology/Microbial Evolution and Genomics, MESH: DNA Transposable Elements, MESH : DNA Transposable Elements, MESH: Recombination, Genetic, escherichia coli, MESH : Likelihood Functions, Research Article, lcsh:QH426-470, MESH : Genome, Bacterial, Biology, Models, Biological, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, MESH: Polymorphism, Genetic, Escherichia coli, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Genome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH : Evolution, Molecular, Gene conversion, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Gene, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Comparative genomics, Polymorphism, Genetic, Evolutionary Biology/Evolutionary and Comparative Genetics, Models, Genetic, 030306 microbiology, génome, MESH : Genomics, MESH: Models, Biological, MESH : Phylogeny, Microbiology/Medical Microbiology, lcsh:Genetics, DNA Transposable Elements, MESH: Likelihood Functions, MESH : Genome, Genome, Bacterial
Abstract

The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome., Author Summary Although abundant knowledge has been accumulated regarding the E. coli laboratory strain K-12, little is known about the evolutionary trajectories that have driven the high diversity observed among natural isolates of the species, which encompass both commensal and highly virulent intestinal and extraintestinal pathogenic strains. We have annotated or re-annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Although recombination rates are much higher than mutation rates, we were able to reconstruct a robust phylogeny based on the ∼2,000 genes common to all strains. Based on this phylogeny, we established the evolutionary scenario of gains and losses of thousands of specific genes, identifying functional classes under opposite selection pressures. This genome flux is confined to very few positions in the chromosome, which are the same for every genome. Notably, we identified few or no extraintestinal virulence-specific genes. We also defined a long-scale structure of recombination in the genome with lower recombination rates at the terminus of replication. These findings demonstrate that, despite a very high gene flow, genes can co-exist in an organised genome.

Published
2009

5. Hypoxia-activated genes from early placenta are elevated in preeclampsia, but not in Intra-Uterine Growth Retardation

Author

Vincent Sapin, Alexandra Garcès-Duran, Bruno Carbonne, Thérèse-Marie Mignot, Françoise Mondon, Virginie Rigourd, Jean-Louis Danan, François Piumi, Daniel Vaiman, R. Rebourcet, Hélène Jammes, Françoise Ferré, Sonia T. Chelbi, Brigitte Robert, Frédérique Quetin, Geoffrey Marceau, ProdInra, Migration, Unité de recherche Génétique Biochimique et Cytogénétique (LGBC), Institut National de la Recherche Agronomique (INRA), Génomique et épigénétique des pathologies placentaires (Inserm U709), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Biologie du développement et reproduction (BDR), École nationale vétérinaire - Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Interactions génétiques et cellulaires au cours de la différenciation, Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de radiobiologie et d'étude du génome (LREG), Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biologie des Transporteurs Mitochondriaux et Métabolisme (BIOTRAM), Centre National de la Recherche Scientifique (CNRS), Service de réanimation néonatale, Institut de Puériculture et de Périnatalogie, CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5), Centre National de la Recherche Scientifique (CNRS)-École nationale vétérinaire d'Alfort (ENVA)-Institut National de la Recherche Agronomique (INRA), Génomique et épigénétique des pathologies placentaires ( Inserm U709 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Département de génétique animale, Institut National de la Recherche Agronomique ( INRA ), Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Laboratoire de radiobiologie et d'étude du génome ( LREG ), Institut National de la Recherche Agronomique ( INRA ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Centre de recherche sur l'endocrinologie moléculaire et le développement ( CREMD ), Centre National de la Recherche Scientifique ( CNRS ), Service de gynécologie-obstétrique, Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Assistance publique - Hôpitaux de Paris (AP-HP)-CHU Saint-Antoine [APHP], The sequencing service of the Cochin platform is greatly acknowledged. This work was funded by INSERM., Laboratoire de Génétique et Biologie Cellulaires (LGBC), Université de la Méditerranée - Aix-Marseille 2-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de recherche sur l'endocrinologie moléculaire et le développement (CREMD), Service de gynécologie-obstétrique [Saint-Antoine], Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Saint-Antoine [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Service de gynécologie-obstétrique [CHU Saint-Antoine], and Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Saint-Antoine [APHP]

Subjects
Swine, Placenta, 0302 clinical medicine, Pregnancy, MESH: Animals, MESH: Models, Genetic, Hypoxia, [ SDV.MHEP.GEO ] Life Sciences [q-bio]/Human health and pathology/Gynecology and obstetrics, ComputingMilieux_MISCELLANEOUS, Oligonucleotide Array Sequence Analysis, 0303 health sciences, 030219 obstetrics & reproductive medicine, Fetal Growth Retardation, MESH : Gene Expression Regulation, Nucleic Acid Hybridization, MESH: Nu, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Multigene Family, medicine.medical_specialty, MESH : Anoxia, MESH: Mitochondria, lcsh:Biotechnology, MESH: Fetal Growth Retardation, MESH : Multigene Family, reproduction, 03 medical and health sciences, Cytogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Complementary DNA, MESH: Gene Library, Genetics, MESH : Cluster Analysis, Humans, MESH : Fetal Growth Retardation, Gene Library, [SDV.GEN]Life Sciences [q-bio]/Genetics, MESH: Humans, Models, Statistical, MESH : Humans, MESH: Adult, MESH: Cluster Analysis, MESH : Nu, MESH: Multigene Family, MESH: Chromosomes, [ SDV.GEN ] Life Sciences [q-bio]/Genetics, MESH: Female, MESH: Models, Statistical, MESH : DNA, Complementary, MESH: Anoxia, MESH : Models, Genetic, [SDV.GEN] Life Sciences [q-bio]/Genetics, Pre-Eclampsia, Cluster Analysis, MESH : Female, Genomic library, Promoter Regions, Genetic, 2. Zero hunger, MESH: Kinetics, MESH : Models, Statistical, MESH : Adult, MESH: Gene Expression Regulation, Mitochondria, medicine.anatomical_structure, Female, MESH : Mitochondria, MESH : Kinetics, DNA microarray, Biotechnology, Research Article, Adult, MESH : Chromosomes, DNA, Complementary, expression génique, lcsh:QH426-470, [SDV.MHEP.GEO]Life Sciences [q-bio]/Human health and pathology/Gynecology and obstetrics, Biology, Chromosomes, MESH : Cytogenetics, gestation, lcsh:TP248.13-248.65, medicine, Animals, Gene, MESH: Cytogenetics, 030304 developmental biology, Models, Genetic, hypoxie, MESH: DNA, Complementary, MESH : Gene Library, Molecular biology, lcsh:Genetics, Kinetics, Gene Expression Regulation, Suppression subtractive hybridization, RNA, MESH : Animals, Genomic imprinting, Poly A
Abstract

Background As a first step to explore the possible relationships existing between the effects of low oxygen pressure in the first trimester placenta and placental pathologies developing from mid-gestation, two subtracted libraries totaling 2304 cDNA clones were constructed. For achieving this, two reciprocal suppressive/subtractive hybridization procedures (SSH) were applied to early (11 weeks) human placental villi after incubation either in normoxic or in hypoxic conditions. The clones from both libraries (1440 hypoxia-specific and 864 normoxia-specific) were spotted on nylon macroarrays. Complex cDNAs probes prepared from placental villi (either from early pregnancy, after hypoxic or normoxic culture conditions, or near term for controls or pathological placentas) were hybridized to the membranes. Results Three hundred and fifty nine clones presenting a hybridization signal above the background were sequenced and shown to correspond to 276 different genes. Nine of these genes are mitochondrial, while 267 are nuclear. Specific expression profiles characteristic of preeclampsia (PE) could be identified, as well as profiles specific of intra-uterine growth retardation (IUGR). Focusing on the chromosomal distribution of the fraction of genes that responded in at least one hybridization experiment, we could observe a highly significant chromosomal clustering of 54 genes into 8 chromosomal regions, four of which containing imprinted genes. Comparative mapping data indicate that these imprinted clusters are maintained in synteny in mice, and apparently in cattle and pigs, suggesting that the maintenance of such syntenies is requested for achieving a normal placental physiology in eutherian mammals. Conclusion We could demonstrate that genes induced in PE were also genes highly expressed under hypoxic conditions (P = 5.10-5), which was not the case for isolated IUGR. Highly expressed placental genes may be in syntenies conserved interspecifically, suggesting that the maintenance of such clusters is requested for achieving a normal placental physiology in eutherian mammals.

Published
2005

6. Identification, characterization and metagenome analysis of oocyte-specific genes organized in clusters in the mouse genome

Author

Sébastien Dadé, Isabelle Callebaut, Martine Bontoux, Amélie Paillisson, Rozenn Dalbies-Tran, Daniel Vaiman, Philippe Monget, Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Laboratoire de minéralogie, cristallographie de Paris (LMCP), Université Pierre et Marie Curie - Paris 6 (UPMC)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Génomique et épigénétique des pathologies placentaires (Inserm U709), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Institut de minéralogie et de physique des milieux condensés (IMPMC), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Physiologie de la reproduction et des comportements [Nouzilly] ( PRC ), Institut National de la Recherche Agronomique ( INRA ) -Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de minéralogie, cristallographie de Paris ( LMCP ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IPG PARIS-Université Paris Diderot - Paris 7 ( UPD7 ) -Centre National de la Recherche Scientifique ( CNRS ), Génomique et épigénétique des pathologies placentaires ( Inserm U709 ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Paris Descartes - Paris 5 ( UPD5 ), Maylin, Françoise, Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Diderot - Paris 7 (UPD7)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS), and Institut de minéralogie et de physique des milieux condensés ( IMPMC )

Subjects
Male, [SDV]Life Sciences [q-bio], MESH : Models, Genetic, Pregnancy Proteins, souris, Genome, Protein Structure, Secondary, MESH : Protein Structure, MESH: Nucleic Acid Hybridization, Mice, Testis, Cluster Analysis, MESH : Female, Tissue Distribution, MESH: Animals, MESH: Models, Genetic, cluster, ComputingMilieux_MISCELLANEOUS, In Situ Hybridization, Genetics, 0303 health sciences, MESH: Pregnancy Proteins, Reverse Transcriptase Polymerase Chain Reaction, MESH: Genomics, 030302 biochemistry & molecular biology, MESH : In Situ Hybridization, Chromosome Mapping, Nucleic Acid Hybridization, Genomics, ovocyte, mus musculus, MESH : Nucleic Acid Hybridization, [ SDV.BBM.GTP ] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Multigene Family, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Female, DNA microarray, Biotechnology, Research Article, expression des gènes, MESH: Computational Biology, lcsh:QH426-470, lcsh:Biotechnology, MESH : Male, In silico, MESH : Multigene Family, RT-PCR, Chromosome 9, Biology, MESH: Oocytes, 03 medical and health sciences, MESH: In Situ Hybridization, femelle, lcsh:TP248.13-248.65, Chromosome 19, Proto-Oncogene Proteins, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MESH : Mice, MESH : Cluster Analysis, Animals, [INFO]Computer Science [cs], MESH: Genome, RNA, Messenger, MESH : Pregnancy Proteins, Gene, MESH: Mice, Chromosome 12, 030304 developmental biology, Models, Genetic, rongeur, génome, MESH : Oocytes, MESH : Genomics, MESH : Fertilization, Chromosome, Computational Biology, MESH: Cluster Analysis, MESH: Male, Protein Structure, Tertiary, lcsh:Genetics, MESH: Protein Structure, Fertilization, Oocytes, identification, MESH: Multigene Family, hybridation in situ, MESH: Fertilization, MESH : Animals, MESH : Genome, MESH: Chromosome Mapping, MESH: Female, MESH : Chromosome Mapping, MESH : Computational Biology
Abstract

Background Genes specifically expressed in the oocyte play key roles in oogenesis, ovarian folliculogenesis, fertilization and/or early embryonic development. In an attempt to identify novel oocyte-specific genes in the mouse, we have used an in silico subtraction methodology, and we have focused our attention on genes that are organized in genomic clusters. Results In the present work, five clusters have been studied: a cluster of thirteen genes characterized by an F-box domain localized on chromosome 9, a cluster of six genes related to T-cell leukaemia/lymphoma protein 1 (Tcl1) on chromosome 12, a cluster composed of a SPErm-associated glutamate (E)-Rich (Speer) protein expressed in the oocyte in the vicinity of four unknown genes specifically expressed in the testis on chromosome 14, a cluster composed of the oocyte secreted protein-1 (Oosp-1) gene and two Oosp-related genes on chromosome 19, all three being characterized by a partial N-terminal zona pellucida-like domain, and another small cluster of two genes on chromosome 19 as well, composed of a TWIK-Related spinal cord K+ channel encoding-gene, and an unknown gene predicted in silico to be testis-specific. The specificity of expression was confirmed by RT-PCR and in situ hybridization for eight and five of them, respectively. Finally, we showed by comparing all of the isolated and clustered oocyte-specific genes identified so far in the mouse genome, that the oocyte-specific clusters are significantly closer to telomeres than isolated oocyte-specific genes are. Conclusion We have studied five clusters of genes specifically expressed in female, some of them being also expressed in male germ-cells. Moreover, contrarily to non-clustered oocyte-specific genes, those that are organized in clusters tend to map near chromosome ends, suggesting that this specific near-telomere position of oocyte-clusters in rodents could constitute an evolutionary advantage. Understanding the biological benefits of such an organization as well as the mechanisms leading to a specific oocyte expression in these clusters now requires further investigation.

Published
2005

7. The BTB/POZ domain of the regulatory proteins Bric à brac 1 (BAB1) and Bric à brac 2 (BAB2) interacts with the novel Drosophila TAF(II) factor BIP2/dTAF(II)155

Author

Jan Larsson, Jean-Christophe Pointud, Bernard Dastugue, Jean-Louis Couderc, Interactions génétiques et cellulaires au cours de la différenciation, Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of microbiology, Umeå University, Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), and Couderc, Jean-Louis

Subjects
MESH : Molecular Sequence Data, Time Factors, MESH : Transcription Factors, Transcription, Genetic, MESH: Drosophila, MESH : Models, Genetic, Plasma protein binding, MESH : Blotting, Western, MESH: Protein Structure, Tertiary, Protein structure, Transcription (biology), Transcriptional regulation, Drosophila Proteins, MESH: Animals, transcriptional regulation, MESH: Models, Genetic, BTB/POZ domain, TAFII, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Genetics, MESH : Blotting, Northern, MESH : Protein Binding, MESH: Transcription Factors, DNA-Binding Proteins, MESH: Repressor Proteins, Drosophila, MESH : DNA-Binding Proteins, MESH : Repressor Proteins, MESH : Protein Structure, Tertiary, Drosophila Protein, MESH : Time Factors, Plasmids, Protein Binding, MESH: Drosophila Proteins, Blotting, Western, Molecular Sequence Data, Biology, MESH: Two-Hybrid System Techniques, Chromatin remodeling, MESH: Plasmids, Two-Hybrid System Techniques, [SDV.BDD] Life Sciences [q-bio]/Development Biology, MESH: Blotting, Northern, MESH: Blotting, Western, MESH: Protein Binding, Animals, [ SDV.BDD ] Life Sciences [q-bio]/Development Biology, MESH : Drosophila, Transcription factor, Molecular Biology, MESH: Molecular Sequence Data, Models, Genetic, MESH: Transcription, Genetic, MESH: Time Factors, MESH : Transcription, Genetic, Cell Biology, MESH : Drosophila Proteins, Blotting, Northern, Protein Structure, Tertiary, Repressor Proteins, MESH : Two-Hybrid System Techniques, MESH : Plasmids, MESH : Animals, MESH: DNA-Binding Proteins, Developmental Biology, Transcription Factors
Abstract

International audience; The BTB/POZ domain is an evolutionarily conserved protein-protein interaction domain present in the N-terminal region of numerous transcription factors involved in development, chromatin remodeling, and human cancers. This domain is involved in homomeric and heteromeric associations with other BTB/POZ domains. The Drosophila BTB/POZ proteins Bric ?rac 1 (BAB1) and Bric ?rac 2 (BAB2) are developmentally regulated transcription factors which are involved in pattern formation along the proximo-distal axis of the leg and antenna, in the morphogenesis of the adult ovaries, and in the control of sexually dimorphic characters. We have identified partners of the BAB1 protein by using the two-hybrid system. The characterization of one of these proteins, called BIP2 for BAB Interacting Protein 2, is presented. BIP2 is a novel Drosophila TATA-box Protein Associated Factor (TAF(II)), also named dTAF(II)155. We show that the BTB/POZ domains of BAB1 and BAB2 are sufficient to mediate a direct interaction with BIP2/dTAF(II)155. This provides a direct link between these BTB/POZ transcription factors and the basal transcriptional machinery. We discuss the implications of the interaction between a BTB/POZ domain and a TAF(II) for the molecular mechanisms of transcriptional control mediated by BTB/POZ transcription factors.

Published
2001

8. RNAi-directed assembly of heterochromatin in fission yeast

Author

André Verdel, Danesh Moazed, Verdel, Andre, Department of cell biology, and Harvard Medical School [Boston] ( HMS )

Subjects
Euchromatin, MESH : Models, Genetic, [SDV.GEN] Life Sciences [q-bio]/Genetics, MESH : Models, Biological, MESH : RNA, Small Interfering, Biochemistry, Histone methylation, Histones, Structural Biology, Heterochromatin, MESH : RNA, RNA, Small Interfering, Heterochromatin assembly, Genetics, Genome, MESH : Chromatin, MESH : Histone Deacetylases, EZH2, Clr4, Chromatin, Transcriptional gene silencing, MESH : Lysine, MESH : RNA Replicase, RNA Interference, Epigenetics, RNA Polymerase II, MESH : RNA Polymerase II, RNA-induced transcriptional silencing, Biophysics, RITS, Biology, Methylation, Models, Biological, Histone Deacetylases, Schizosaccharomyces, Animals, MESH : Histones, Molecular Biology, RNA, Double-Stranded, Histone binding, Models, Genetic, MESH : Heterochromatin, Lysine, fungi, MESH : RNA, Double-Stranded, Cell Biology, MESH : Methylation, RNA-Dependent RNA Polymerase, MESH : Schizosaccharomyces, RNAi, RNA, Heterochromatin protein 1, MESH : Animals, MESH : RNA Interference, MESH : Genome, [ SDV.GEN ] Life Sciences [q-bio]/Genetics
Abstract

International audience; Heterochromatin is an epigenetically heritable and conserved feature of eukaryotic chromosomes with important roles in chromosome segregation, genome stability, and gene regulation. The formation of heterochromatin involves an ordered array of chromatin changes, including histone deacetylation, histone H3-lysine 9 methylation, and recruitment of histone binding proteins such as Swi6/HP1. Recent discoveries have uncovered a role for the RNA interference (RNAi) pathway in heterochromatin assembly in the fission yeast Schizosaccharomyces pombe and other eukaryotes. Purification of two RNAi complexes, RITS and RDRC, from fission yeast has provided further insight into the mechanism of RNAi-mediated heterochromatin assembly. These discoveries have given rise to a model in which small interfering RNA molecules act as specificity factors that initiate epigenetic chromatin modifications and double strand RNA synthesis at specific chromosome regions.

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9. Cloning, sequencing, and characterization of five genes coding for Acyl-CoA oxidase isozymes in the yeast Yarrowia lipolytica

Author

M.-T. Le Dall, Jean-Marc Nicaud, Jean-Marc Belin, Céline Laroche, Yves Waché, Huijie Wang, Microbiologie et Génétique Moléculaire ( MGM ), Institut National de la Recherche Agronomique ( INRA ) -Institut National Agronomique Paris-Grignon ( INA P-G ) -Centre National de la Recherche Scientifique ( CNRS ), Laboratoire de Microbiologie, UMR INRA 1082, AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Génie des Procédés Microbiologiques et Alimentaires ( GPMA ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire de Microbioologie, UMR INRA 1283 Ecole Nationale Supérieure de Biologie Appliquée à la. Nutrition et à l'Alimentation, Institut National de la Recherche Agronomique ( INRA ), Collection de Levures d'Intérêt Biotechnologique et Laboratoire de Génétique Moléculaire et Cellulaire, Institut National de la Recherche Agronomique ( INRA ) -Centre National de la Recherche Scientifique ( CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Microbiologie et Génétique Moléculaire (MGM), Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G)-Centre National de la Recherche Scientifique (CNRS), Génie des Procédés Microbiologiques et Alimentaires (GPMA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire de Microbioologie, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA), and Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, MESH : Molecular Sequence Data, MESH: Sequence Homology, Amino Acid, Sequence Homology, MESH : Models, Genetic, MESH: Amino Acid Sequence, Biochemistry, Polymerase Chain Reaction, Models, Yeasts, Acyl-CoA oxidase, MESH: Models, Genetic, Cloning, Molecular, [INFO.INFO-BT]Computer Science [cs]/Biotechnology, MESH : Polymerase Chain Reaction, MESH : Fatty Acids, Genetics, MESH : Isoenzymes, 0303 health sciences, Oxidase test, biology, MESH: Yeasts, MESH : Amino Acid Sequence, Fatty Acids, MESH: Acyl-CoA Oxidase, General Medicine, Peroxisome, MESH : Oxidoreductases, MESH : Sequence Homology, Amino Acid, 3. Good health, MESH: Fatty Acids, Isoenzymes, Amino Acid, Fungal, MESH: Isoenzymes, MESH : Acyl-CoA Oxidase, Oxidoreductases, [ INFO.INFO-BT ] Computer Science [cs]/Biotechnology, MESH : Cloning, Molecular, Genes, Fungal, Molecular Sequence Data, Biophysics, Isozyme, 03 medical and health sciences, Genetic, Insertional, Peroxisomes, MESH: Cloning, Molecular, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, MESH: Oxidoreductases, Gene, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, 030304 developmental biology, Cloning, MESH : Yeasts, MESH : Mutagenesis, Insertional, MESH: Molecular Sequence Data, Models, Genetic, Sequence Homology, Amino Acid, 030306 microbiology, Molecular, [ SDV.BIO ] Life Sciences [q-bio]/Biotechnology, Yarrowia, MESH: Polymerase Chain Reaction, Cell Biology, biology.organism_classification, Yeast, MESH: Peroxisomes, Mutagenesis, Insertional, Genes, MESH: Mutagenesis, Insertional, Mutagenesis, Acyl-CoA Oxidase, MESH : Genes, Fungal, MESH: Genes, Fungal, MESH : Peroxisomes
Abstract

International audience; The Acyl-CoA oxidase (AOX) isozymes catalyze the first steps of peroxisomal beta-oxidation, which is important for the degradation of fatty acids. Using conserved blocks in previously identified yeast POX genes encoding AOXs, the authors have shown that five POX genes are present in the yeast Yarrowia lipolytica. These genes show approx 63% identity among themselves, and 42% identity with the POX genes from other yeasts. Mono-disrupted Y. lipolytica strains were constructed using a variation of the sticky-end polymerase chain reaction method. AOX activity in the mono-disrupted strains revealed that a long-chain oxidase is encoded by the POX2 gene and a short-chain oxidase by the POX3 gene.

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