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3. Phenotypic Differences Between Polygenic and Monogenic Hypobetalipoproteinemia

Author

Rimbert, Antoine, Vanhoye, Xavier, Coulibaly, Dramane, Marrec, Marie, Pichelin, Matthieu, Charrière, Sybil, Peretti, Noël, Valéro, René, Wargny, Matthieu, Carrié, Alain, Lindenbaum, Pierre, Deleuze, Jean-François, Genin, Emmanuelle, Redon, Richard, Rollat-Farnier, Pierre Antoine, Goxe, Didier, Degraef, Gilles, Marmontel, Oriane, Divry, Eléonore, Bigot-Corbel, Edith, Moulin, Philippe, Cariou, Bertrand, and Di Filippo, Mathilde

Published
2020
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4. Molecular investigation, using chromosomal microarray and whole exome sequencing, of six patients affected by Williams Beuren syndrome and Autism Spectrum Disorder

Author

Masson, Julie, Demily, Caroline, Chatron, Nicolas, Labalme, Audrey, Rollat-Farnier, Pierre-Antoine, Schluth-Bolard, Caroline, Gilbert-Dussardier, Brigitte, Giuliano, Fabienne, Touraine, Renaud, Tordjman, Sylvie, Verloes, Alain, Testa, Giuseppe, Sanlaville, Damien, Edery, Patrick, Lesca, Gaetan, and Rossi, Massimiliano

Published
2019
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5. Familial transmission of chromoanagenesis leads to unpredictable unbalanced rearrangements through meiotic recombination

Author

Masson, Julie, primary, Pebrel‐Richard, Céline, additional, Egloff, Matthieu, additional, Frétigny, Mathilde, additional, Beaumont, Marion, additional, Uguen, Kevin, additional, Rollat‐Farnier, Pierre‐Antoine, additional, Diguet, Flavie, additional, Perthus, Isabelle, additional, Le Gudayer, Gwenaël, additional, Haye, Damien, additional, Dupeyron, Marie‐Noëlle Bonnet, additional, Putoux, Audrey, additional, Raskin‐Champion, Fabienne, additional, Till, Marianne, additional, Chatron, Nicolas, additional, Doray, Bérénice, additional, Bardel, Claire, additional, Vinciguerra, Christine, additional, Sanlaville, Damien, additional, and Schluth‐Bolard, Caroline, additional

Published
2023
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6. Alpha Satellite Insertion Close to an Ancestral Centromeric Region

Author

Giannuzzi, Giuliana, Logsdon, Glennis A, Chatron, Nicolas, Miller, Danny E, Reversat, Julie, Munson, Katherine M, Hoekzema, Kendra, Bonnet-Dupeyron, Marie-Noëlle, Rollat-Farnier, Pierre-Antoine, Baker, Carl A, Sanlaville, Damien, Eichler, Evan E, Schluth-Bolard, Caroline, and Reymond, Alexandre

Subjects
Chromosomal Proteins, Non-Histone, ancestral centromere, Centromere, AcademicSubjects/SCI01130, structural variation, Humans, alpha satellite, DNA, Satellite, AcademicSubjects/SCI01180, Centromere Protein B, Discoveries, In Situ Hybridization, Fluorescence
Abstract

Human centromeres are mainly composed of alpha satellite DNA hierarchically organized as higher-order repeats (HORs). Alpha satellite dynamics is shown by sequence homogenization in centromeric arrays and by its transfer to other centromeric locations, for example, during the maturation of new centromeres. We identified during prenatal aneuploidy diagnosis by fluorescent in situ hybridization a de novo insertion of alpha satellite DNA from the centromere of chromosome 18 (D18Z1) into cytoband 15q26. Although bound by CENP-B, this locus did not acquire centromeric functionality as demonstrated by the lack of constriction and the absence of CENP-A binding. The insertion was associated with a 2.8-kbp deletion and likely occurred in the paternal germline. The site was enriched in long terminal repeats and located ∼10 Mbp from the location where a centromere was ancestrally seeded and became inactive in the common ancestor of humans and apes 20–25 million years ago. Long-read mapping to the T2T-CHM13 human genome assembly revealed that the insertion derives from a specific region of chromosome 18 centromeric 12-mer HOR array in which the monomer size follows a regular pattern. The rearrangement did not directly disrupt any gene or predicted regulatory element and did not alter the methylation status of the surrounding region, consistent with the absence of phenotypic consequences in the carrier. This case demonstrates a likely rare but new class of structural variation that we name “alpha satellite insertion.” It also expands our knowledge on alphoid DNA dynamics and conveys the possibility that alphoid arrays can relocate near vestigial centromeric sites.

Published
2021

7. Whole exome sequencing in three families segregating a pediatric case of sarcoidosis

Author

Calender, Alain, Rollat Farnier, Pierre Antoine, Buisson, Adrien, Pinson, Stéphane, Bentaher, Abderrazzaq, Lebecque, Serge, Corvol, Harriet, Abou Taam, Rola, Houdouin, Véronique, Bardel, Claire, Roy, Pascal, Devouassoux, Gilles, Cottin, Vincent, Seve, Pascal, Bernaudin, Jean-François, Lim, Clarice X., Weichhart, Thomas, Valeyre, Dominique, Pacheco, Yves, Clement, Annick, Nathan, Nadia, and in the frame of GSF (Groupe Sarcoïdose France)

Published
2018
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8. Development of a new expanded next‐generation sequencing panel for genetic diseases involved in dyslipidemia

Author

Marmontel, Oriane, primary, Rollat‐Farnier, Pierre Antoine, additional, Wozny, Anne‐Sophie, additional, Charrière, Sybil, additional, Vanhoye, Xavier, additional, Simonet, Thomas, additional, Chatron, Nicolas, additional, Collin‐Chavagnac, Delphine, additional, Nony, Séverine, additional, Dumont, Sabrina, additional, Mahl, Muriel, additional, Jacobs, Chantal, additional, Janin, Alexandre, additional, Caussy, Cyrielle, additional, Poinsot, Pierre, additional, Tauveron, Igor, additional, Bardel, Claire, additional, Millat, Gilles, additional, Peretti, Noël, additional, Moulin, Philippe, additional, Marçais, Christophe, additional, and Di Filippo, Mathilde, additional

Published
2020
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9. Genome sequencing in cytogenetics: Comparison of short‐read and linked‐read approaches for germline structural variant detection and characterization

Author

Uguen, Kévin, Jubin, Claire, Duffourd, Yannis, Bardel, Claire, Malan, Valérie, Dupont, Jean‐Michel, El Khattabi, Laila, Chatron, Nicolas, Vitobello, Antonio, Rollat‐Farnier, Pierre‐Antoine, Baulard, Céline, Lelorch, Marc, Leduc, Aurelie, Tisserant, Emilie, Tran Mau‐Them, Frédéric, Danjean, Vincent, Délépine, Marc, Till, Marianne, Meyer, Vincent, LYONNET, Stanislas, Mosca‐Boidron, Anne‐laure, Thevenon, Julien, Faivre, Laurence, Thauvin‐Robinet, Christel, Schluth‐Bolard, Caroline, Boland, Anne, Olaso, Robert, Callier, Patrick, Romana, Serge, Deleuze, Jean‐François, Sanlaville, Damien, Génétique, génomique fonctionnelle et biotechnologies (UMR 1078) (GGB), EFS-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO), 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), Equipe GAD (LNC - U1231), Lipides - Nutrition - Cancer [Dijon - U1231] (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre Albert Trillat [Hôpital de la Croix-Rousse - HCL], Hôpital de la Croix-Rousse [CHU - HCL], Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Laboratoire Histologie Embryologie Cytogénétique [CHU Necker], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de Génotypage (CNG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Performance analysis and optimization of LARge Infrastructures and Systems (POLARIS), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Grenoble (LIG), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Service de génétique [Hôpial Louis Pradel - HCL], Hôpital Louis Pradel [CHU - HCL], Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Pôle Couple-Enfant, Département de Génétique et Procréation, Centre de génétique - Centre de référence des maladies rares, anomalies du développement et syndromes malformatifs (CHU de Dijon), Centre Hospitalier Universitaire de Dijon - Hôpital François Mitterrand (CHU Dijon), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO)-Université de Brest (UBO)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Centre de recherche en neurosciences de Lyon (CRNL), Université de Lyon-Université de Lyon-Université Jean Monnet [Saint-Étienne] (UJM)-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)-Université de Paris (UP), Génétique des Anomalies du Développement (GAD), IFR100 - Structure fédérative de recherche Santé-STIC-Université de Bourgogne (UB), Eco-Anthropologie et Ethnobiologie (EAE), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Cytogénétique, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP], Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Unité Mathématique, Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Laboratoire d'Informatique de Grenoble (LIG), Université Pierre Mendès France - Grenoble 2 (UPMF)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut National Polytechnique de Grenoble (INPG)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Service de cytogénétique constitutionnelle, Hospices Civils de Lyon (HCL)-CHU de Lyon-Centre Neuroscience et Recherche, Laboratoire Information, Milieux, Médias, Médiations - EA 3820 (I3M), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Université de Toulon (UTLN), Génétique et épigénétique des maladies métaboliques, neurosensorielles et du développement (Inserm U781), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Lipides - Nutrition - Cancer (U866) (LNC), Université de Bourgogne (UB)-Institut National de la Santé et de la Recherche Médicale (INSERM)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Ecole Nationale Supérieure de Biologie Appliquée à la Nutrition et à l'Alimentation de Dijon (ENSBANA), Service d'Histologie-Embryologie et Cytogénétique Assistance Publique, Assistance publique - Hôpitaux de Paris (AP-HP) (APHP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC)

Subjects
Whole Genome Sequencing, lcsh:QH426-470, Method, structural variants, Chromosome Disorders, bioinformatics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], genome sequencing, Cytogenetics, lcsh:Genetics, 10X Genomics: Illumina, Intellectual Disability, Genomic Structural Variation, Humans, Abnormalities, Multiple, Genetic Testing, Germ-Line Mutation, ComputingMilieux_MISCELLANEOUS
Abstract

Background Structural variants (SVs) include copy number variants (CNVs) and apparently balanced chromosomal rearrangements (ABCRs). Genome sequencing (GS) enables SV detection at base‐pair resolution, but the use of short‐read sequencing is limited by repetitive sequences, and long‐read approaches are not yet validated for diagnosis. Recently, 10X Genomics proposed Chromium, a technology providing linked‐reads to reconstruct long DNA fragments and which could represent a good alternative. No study has compared short‐read to linked‐read technologies to detect SVs in a constitutional diagnostic setting yet. The aim of this work was to determine whether the 10X Genomics technology enables better detection and comprehension of SVs than short‐read WGS. Methods We included 13 patients carrying various SVs. Whole genome analyses were performed using paired‐end HiSeq X sequencing with (linked‐read strategy) or without (short‐read strategy) Chromium library preparation. Two different bioinformatic pipelines were used: Variants are called using BreakDancer for short‐read strategy and LongRanger for long‐read strategy. Variant interpretations were first blinded. Results The short‐read strategy allowed diagnosis of known SV in 10/13 patients. After unblinding, the linked‐read strategy identified 10/13 SVs, including one (patient 7) missed by the short‐read strategy. Conclusion In conclusion, regarding the results of this study, 10X Genomics solution did not improve the detection and characterization of SV., We compared linked‐read and short‐read sequencing in patients with structural variants. We conclude that linked‐read strategy did not improve the detection and characterization of structural variants.

Published
2020
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10. Fryns type mesomelic dysplasia of the upper limbs caused by inverted duplications of the HOXD gene cluster

Author

Le Caignec, Cédric, primary, Pichon, Olivier, additional, Briand, Annaig, additional, de Courtivron, Benoît, additional, Bonnard, Christian, additional, Lindenbaum, Pierre, additional, Redon, Richard, additional, Schluth-Bolard, Caroline, additional, Diguet, Flavie, additional, Rollat-Farnier, Pierre-Antoine, additional, Sanchez-Castro, Marta, additional, Vuillaume, Marie-Laure, additional, Sanlaville, Damien, additional, Duboule, Denis, additional, Mégarbané, André, additional, and Toutain, Annick, additional

Published
2019
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11. Exome sequencing and pathogenicity-network analysis of five French families implicate mTOR signalling and autophagy in familial sarcoidosis

Author

Calender, Alain, primary, Lim, Clarice X., additional, Weichhart, Thomas, additional, Buisson, Adrien, additional, Besnard, Valérie, additional, Rollat-Farnier, Pierre Antoine, additional, Bardel, Claire, additional, Roy, Pascal, additional, Cottin, Vincent, additional, Devouassoux, Gilles, additional, Finat, Amélie, additional, Pinson, Stéphane, additional, Lebecque, Serge, additional, Nunes, Hilario, additional, Israel-Biet, Dominique, additional, Bentaher, Abderazzaq, additional, Valeyre, Dominique, additional, and Pacheco, Yves, additional

Published
2019
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12. Whole genome paired-end sequencing elucidates functional and phenotypic consequences of balanced chromosomal rearrangement in patients with developmental disorders

Author

Schluth-Bolard, Caroline, primary, Diguet, Flavie, additional, Chatron, Nicolas, additional, Rollat-Farnier, Pierre-Antoine, additional, Bardel, Claire, additional, Afenjar, Alexandra, additional, Amblard, Florence, additional, Amiel, Jeanne, additional, Blesson, Sophie, additional, Callier, Patrick, additional, Capri, Yline, additional, Collignon, Patrick, additional, Cordier, Marie-Pierre, additional, Coubes, Christine, additional, Demeer, Benedicte, additional, Chaussenot, Annabelle, additional, Demurger, Florence, additional, Devillard, Françoise, additional, Doco-Fenzy, Martine, additional, Dupont, Céline, additional, Dupont, Jean-Michel, additional, Dupuis-Girod, Sophie, additional, Faivre, Laurence, additional, Gilbert-Dussardier, Brigitte, additional, Guerrot, Anne-Marie, additional, Houlier, Marine, additional, Isidor, Bertrand, additional, Jaillard, Sylvie, additional, Joly-Hélas, Géraldine, additional, Kremer, Valérie, additional, Lacombe, Didier, additional, Le Caignec, Cédric, additional, Lebbar, Aziza, additional, Lebrun, Marine, additional, Lesca, Gaetan, additional, Lespinasse, James, additional, Levy, Jonathan, additional, Malan, Valérie, additional, Mathieu-Dramard, Michele, additional, Masson, Julie, additional, Masurel-Paulet, Alice, additional, Mignot, Cyril, additional, Missirian, Chantal, additional, Morice-Picard, Fanny, additional, Moutton, Sébastien, additional, Nadeau, Gwenaël, additional, Pebrel-Richard, Céline, additional, Odent, Sylvie, additional, Paquis-Flucklinger, Véronique, additional, Pasquier, Laurent, additional, Philip, Nicole, additional, Plutino, Morgane, additional, Pons, Linda, additional, Portnoï, Marie-France, additional, Prieur, Fabienne, additional, Puechberty, Jacques, additional, Putoux, Audrey, additional, Rio, Marlène, additional, Rooryck-Thambo, Caroline, additional, Rossi, Massimiliano, additional, Sarret, Catherine, additional, Satre, Véronique, additional, Siffroi, Jean-Pierre, additional, Till, Marianne, additional, Touraine, Renaud, additional, Toutain, Annick, additional, Toutain, Jérome, additional, Valence, Stéphanie, additional, Verloes, Alain, additional, Whalen, Sandra, additional, Edery, Patrick, additional, Tabet, Anne-Claude, additional, and Sanlaville, Damien, additional

Published
2019
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13. Supravalvular Aortic Stenosis Caused by a Familial Chromosome 7 Inversion Disrupting the ELN Gene Uncovered by Whole-Genome Sequencing

Author

Pons, Linda, primary, Bouvagnet, Patrice, additional, Bakloul, Mohamed, additional, Di Filippo, Sylvie, additional, Buisson, Adrien, additional, Chatron, Nicolas, additional, Labalme, Audrey, additional, Metton, Olivier, additional, Mitchell, Julia, additional, Diguet, Flavie, additional, Rollat-Farnier, Pierre-Antoine, additional, Sanlaville, Damien, additional, and Schluth-Bolard, Caroline, additional

Published
2019
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14. Phenotypic Differences Between Polygenic and Monogenic Hypobetalipoproteinemia.

Author

Rimbert, Antoine, Vanhoye, Xavier, Coulibaly, Dramane, Marrec, Marie, Pichelin, Matthieu, Charrière, Sybil, Peretti, Noël, Valéro, René, Wargny, Matthieu, Carrié, Alain, Lindenbaum, Pierre, Deleuze, Jean-François, Genin, Emmanuelle, Redon, Richard, Rollat-Farnier, Pierre Antoine, Goxe, Didier, Degraef, Gilles, Marmontel, Oriane, Divry, Eléonore, and Bigot-Corbel, Edith

Published
2021
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15. Fryns type mesomelic dysplasia of the upper limbs caused by inverted duplications of the HOXDgene cluster

Author

Le Caignec, Cédric, Pichon, Olivier, Briand, Annaig, de Courtivron, Benoît, Bonnard, Christian, Lindenbaum, Pierre, Redon, Richard, Schluth-Bolard, Caroline, Diguet, Flavie, Rollat-Farnier, Pierre-Antoine, Sanchez-Castro, Marta, Vuillaume, Marie-Laure, Sanlaville, Damien, Duboule, Denis, Mégarbané, André, and Toutain, Annick

Abstract

The HoxDcluster is critical for vertebrate limb development. Enhancers located in both the telomeric and centromeric gene deserts flanking the cluster regulate the transcription of HoxDgenes. In rare patients, duplications, balanced translocations or inversions misregulating HOXDgenes are responsible for mesomelic dysplasia of the upper and lower limbs. By aCGH, whole-genome mate-pair sequencing, long-range PCR and fiber fluorescent in situ hybridization, we studied patients from two families displaying mesomelic dysplasia limited to the upper limbs. We identified microduplications including the HOXDcluster and showed that microduplications were in an inverted orientation and inserted between the HOXDcluster and the telomeric enhancers. Our results highlight the existence of an autosomal dominant condition consisting of isolated ulnar dysplasia caused by microduplications inserted between the HOXDcluster and the telomeric enhancers. The duplications likely disconnect the HOXD9to HOXD11genes from their regulatory sequences. This presumptive loss-of-function may have contributed to the phenotype. In both cases, however, these rearrangements brought HOXD13closer to telomeric enhancers, suggesting that the alterations derive from the dominant-negative effect of this digit-specific protein when ectopically expressed during the early development of forearms, through the disruption of topologically associating domain structure at the HOXDlocus.

Published
2020
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16. Two Host Clades, Two Bacterial Arsenals: Evolution through Gene Losses in Facultative Endosymbionts

Author

Rollat-Farnier, Pierre-Antoine, Santos-Garcia, Diego, Rao, Qiong, Sagot, Marie-France, Silva, Francisco J, Henri, Hélène, Zchori-Fein, Einat, Latorre, Amparo, Moya, Andrés, Barbe, Valérie, Liu, Shu-Sheng, Wang, Xiao-Wei, Vavre, Fabrice, Mouton, Laurence, Baobab, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), An algorithmic view on genomes, cells, and environments (BAMBOO), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València (UV), Zhejiang Agriculture and Forestry University, Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale (ERABLE), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Agricultural Research Organisation (ARO), Volcani Center, Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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)-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 et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), and European Project: 247073,EC:FP7:ERC,ERC-2009-AdG,SISYPHE(2010)

Subjects
Hamiltonella defensa, Virulence Factors, [SDV]Life Sciences [q-bio], fungi, food and beverages, Genomics, comparative genomics, biochemical phenomena, metabolism, and nutrition, Bemisia tabaci, Evolution, Molecular, Hemiptera, aphids, Enterobacteriaceae, Cell Wall, Animals, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Symbiosis, Gene Deletion, Genome, Bacterial, Phylogeny, Research Article
Abstract

International audience; Bacterial endosymbiosis is an important evolutionary process in insects, which can harbor both obligate and facultative symbionts. The evolution of these symbionts is driven by evolutionary convergence, and they exhibit among the tiniest genomes in prokaryotes. The large host spectrum of facultative symbionts and the high diversity of strategies they use to infect new hosts probably impact the evolution of their genome and explain why they undergo less severe genomic erosion than obligate symbionts. Candidatus Hamiltonella defensa is suitable for the investigation of the genomic evolution of facultative symbionts because the bacteria are engaged in specific relationships in two clades of insects. In aphids, H. defensa is found in several species with an intermediate prevalence and confers protection against parasitoids. In whiteflies, H. defensa is almost fixed in some species of Bemisia tabaci, which suggests an important role of and a transition toward obligate symbiosis. In this study, comparisons of the genome of H. defensa present in two B. tabaci species (Middle East Asia Minor 1 and Mediterranean) and in the aphid Acyrthosiphon pisum revealed that they belong to two distinct clades and underwent specific gene losses. In aphids, it contains highly virulent factors that could allow protection and horizontal transfers. In whiteflies, the genome lost these factors and seems to have a limited ability to acquire genes. However it contains genes that could be involved in the production of essential nutrients, which is consistent with a primordial role for this symbiont. In conclusion, although both lineages of H. defensa have mutualistic interactions with their hosts, their genomes follow distinct evolutionary trajectories that reflect their phenotype and could have important consequences on their evolvability.

Published
2015
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17. Supravalvular Aortic Stenosis Caused by a Familial Chromosome 7 Inversion Disrupting the ELNGene Uncovered by Whole-Genome Sequencing

Author

Pons, Linda, Bouvagnet, Patrice, Bakloul, Mohamed, Di Filippo, Sylvie, Buisson, Adrien, Chatron, Nicolas, Labalme, Audrey, Metton, Olivier, Mitchell, Julia, Diguet, Flavie, Rollat-Farnier, Pierre-Antoine, Sanlaville, Damien, and Schluth-Bolard, Caroline

Abstract

Apparently, balanced chromosomal rearrangements usually have no phenotypic consequences for the carrier. However, in some cases, they may be associated with an abnormal phenotype. We report herein the case of a 4-year-old boy presenting with clinically isolated supravalvular aortic stenosis (SVAS). No chromosomal imbalance was detected by array CGH. The karyotype showed a balanced paracentric chromosome 7 inversion. Breakpoint characterization using paired-end whole-genome sequencing (WGS) revealed an ELN gene disruption in intron 1, accounting for the phenotype. Family study showed that the inversion was inherited, with incomplete penetrance. To our knowledge, this is the first case of a disruption of the ELNgene characterized by WGS. It contributes to refine the genotype-phenotype correlation in ELNdisruption. Although this disruption is a rare etiology of SVAS, it cannot be detected by the diagnostic tests usually performed, such as array CGH or sequencing methods (Sanger, panel, or exome sequencing). With the future perspective of WGS as a diagnostic tool, it will be important to include a structural variation analysis in order to detect balanced rearrangements and gene disruption.

Published
2019
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18. Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci

Author

Rao, Qiong, primary, Rollat-Farnier, Pierre-Antoine, additional, Zhu, Dan-Tong, additional, Santos-Garcia, Diego, additional, Silva, Francisco J, additional, Moya, Andrés, additional, Latorre, Amparo, additional, Klein, Cecilia C, additional, Vavre, Fabrice, additional, Sagot, Marie-France, additional, Liu, Shu-Sheng, additional, Mouton, Laurence, additional, and Wang, Xiao-Wei, additional

Published
2015
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20. Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci.

Author

Qiong Rao, Rollat-Farnier, Pierre-Antoine, Dan-Tong Zhu, Santos-Garcia, Diego, Silva, Francisco J., Moya, Andrés, Latorre, Amparo, Klein, Cecilia C., Vavre, Fabrice, Sagot, Marie-France, Shu-Sheng Liu, Mouton, Laurence, and Xiao-Wei Wang

Subjects
*SWEETPOTATO whitefly, *ENTEROBACTERIACEAE, *CANDIDATUS, *INVERTEBRATE-bacteria relationships, *ENDOSYMBIOSIS
Abstract

Background: The whitefly Bemisia tabaci is an important agricultural pest with global distribution. This phloem-sap feeder harbors a primary symbiont, "Candidatus Portiera aleyrodidarum", which compensates for the deficient nutritional composition of its food sources, and a variety of secondary symbionts. Interestingly, all of these secondary symbionts are found in co-localization with the primary symbiont within the same bacteriocytes, which should favor the evolution of strong interactions between symbionts. Results: In this paper, we analyzed the genome sequences ofthe primary symbiont Portiera and ofthe secondary symbiont Hamiltonella in the B. tabaci Mediterranean (MED) species in order to gain insight into the metabolic role of each symbiont in the biology of their host. The genome sequences of the uncultured symbionts Portiera and Hamiltonella were obtained from one single bacteriocyte of MED B. tabaci. As already reported, the genome of Portiera is highly reduced (357 kb), but has kept a number of genes encoding most essential amino-acids and carotenoids. On the other hand, Portiera lacks almost all the genes involved in the synthesis of vitamins and cofactors. Moreover, some pathways are incomplete, notably those involved in the synthesis of some essential amino-acids. Interestingly, the genome of Hamiltonella revealed that this secondary symbiont can not only provide vitamins and cofactors, but also complete the missing steps of some of the pathways of Portiera. In addition, some critical amino-acid biosynthetic genes are missing in the two symbiotic genomes, but analysis of whitefly transcriptome suggests that the missing steps may be performed by the whitefly itself or its microbiota. Conclusions: These data suggest that Portiera and Hamiltonella are not only complementary but could also be mutually dependent to provide a full complement of nutrients to their host. Altogether, these results illustrate how functional redundancies can lead to gene losses in the genomes ofthe different symbiotic partners, reinforcing their inter-dependency. [ABSTRACT FROM AUTHOR]

Published
2015
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21. Fryns type mesomelic dysplasia of the upper limbs caused by inverted duplications of the HOXD gene cluster.

Author

Le Caignec C, Pichon O, Briand A, de Courtivron B, Bonnard C, Lindenbaum P, Redon R, Schluth-Bolard C, Diguet F, Rollat-Farnier PA, Sanchez-Castro M, Vuillaume ML, Sanlaville D, Duboule D, Mégarbané A, and Toutain A

Subjects
Bone Diseases, Developmental pathology, Cells, Cultured, Female, Humans, Infant, Loss of Function Mutation, Male, Multigene Family, Phenotype, Upper Extremity Deformities, Congenital pathology, Bone Diseases, Developmental genetics, Gene Duplication, Homeodomain Proteins genetics, Upper Extremity Deformities, Congenital genetics
Abstract

The HoxD cluster is critical for vertebrate limb development. Enhancers located in both the telomeric and centromeric gene deserts flanking the cluster regulate the transcription of HoxD genes. In rare patients, duplications, balanced translocations or inversions misregulating HOXD genes are responsible for mesomelic dysplasia of the upper and lower limbs. By aCGH, whole-genome mate-pair sequencing, long-range PCR and fiber fluorescent in situ hybridization, we studied patients from two families displaying mesomelic dysplasia limited to the upper limbs. We identified microduplications including the HOXD cluster and showed that microduplications were in an inverted orientation and inserted between the HOXD cluster and the telomeric enhancers. Our results highlight the existence of an autosomal dominant condition consisting of isolated ulnar dysplasia caused by microduplications inserted between the HOXD cluster and the telomeric enhancers. The duplications likely disconnect the HOXD9 to HOXD11 genes from their regulatory sequences. This presumptive loss-of-function may have contributed to the phenotype. In both cases, however, these rearrangements brought HOXD13 closer to telomeric enhancers, suggesting that the alterations derive from the dominant-negative effect of this digit-specific protein when ectopically expressed during the early development of forearms, through the disruption of topologically associating domain structure at the HOXD locus.

Published
2020
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