25 results on '"Gérard, Matthieu"'
Search Results
2. Column generation based approaches for a tour scheduling problem with a multi-skill heterogeneous workforce
- Author
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Gérard, Matthieu, Clautiaux, François, and Sadykov, Ruslan
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- 2016
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3. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells
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de Dieuleveult, Maud, Yen, Kuangyu, Hmitou, Isabelle, Depaux, Arnaud, Boussouar, Fayçal, Dargham, Daria Bou, Jounier, Sylvie, Humbertclaude, Hélène, Ribierre, Florence, Baulard, Céline, Farrell, Nina P., Park, Bongsoo, Keime, Céline, Carrière, Lucie, Berlivet, Soizick, Gut, Marta, Gut, Ivo, Werner, Michel, Deleuze, Jean-François, Olaso, Robert, Aude, Jean-Christophe, Chantalat, Sophie, Pugh, B. Franklin, and Gérard, Matthieu
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- 2016
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4. Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells
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Carrière, Lucie, Graziani, Sébastien, Alibert, Olivier, Ghavi-Helm, Yad, Boussouar, Fayçal, Humbertclaude, Hélène, Jounier, Sylvie, Aude, Jean-Christophe, Keime, Céline, Murvai, Janos, Foglio, Mario, Gut, Marta, Gut, Ivo, Lathrop, Mark, Soutourina, Julie, Gérard, Matthieu, and Werner, Michel
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- 2012
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5. Deletion of a HoxD enhancer induces transcriptional heterochrony leading to transposition of the sacrum
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Zákány, József, Gérard, Matthieu, Favier, Bertrand, and Duboule, Denis
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- 1997
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6. Capucin does not modify the toxicity of a mutant Huntingtin fragment in vivo
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Galvan, Laurie, Lepejová, Nad'a, Gaillard, Marie-Claude, Malgorn, Carole, Guillermier, Martine, Houitte, Diane, Bonvento, Gilles, Petit, Fanny, Dufour, Noëlle, Héry, Patrick, Gérard, Matthieu, Elalouf, Jean-Marc, Déglon, Nicole, Brouillet, Emmanuel, and de Chaldée, Michel
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- 2012
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7. Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells
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Morozumi, Yuichi, Boussouar, Fayçal, Tan, Minjia, Chaikuad, Apirat, Jamshidikia, Mahya, Colak, Gozde, He, Huang, Nie, Litong, Petosa, Carlo, De Dieuleveult, Maud, Curtet, Sandrine, Vitte, Anne-Laure, Rabatel, Clothilde, Debernardi, Alexandra, François-Loïc, Cosset, Verhoeyen, Els, Emadali, Anouk, Schweifer, Norbert, Gianni, Davide, Gut, Marta, Guardiola, Philippe, Rousseaux, Sophie, Gérard, Matthieu, Knapp, Stefan, Zhao, Yingming, Khochbin, Saadi, Institut d'oncologie/développement Albert Bonniot de Grenoble (INSERM U823), Université Joseph Fourier - Grenoble 1 (UJF)-CHU Grenoble-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Structural Genomics Consortium, University of Oxford, Nuffield Department of Clinical Medicine [Oxford], Ben May Department of Cancer Research, The University of Chicago Medicine, Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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), 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), Virus enveloppés, vecteurs et immunothérapie – Enveloped viruses, Vectors and Immuno-therapy (EVIR), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-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)-École normale supérieure de Lyon (ENS de Lyon)-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), Equipe 'Contrôle Métabolique des Morts Cellulaires' (INSERM U1065 - C3M), Centre méditerranéen de médecine moléculaire (C3M), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Côte d'Azur (UCA), Boehringer Ingelheim RCV, Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Centre de Recherche en Cancérologie Nantes-Angers (CRCNA), Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM)-Hôtel-Dieu de Nantes-Institut National de la Santé et de la Recherche Médicale (INSERM)-Hôpital Laennec-Centre National de la Recherche Scientifique (CNRS)-Faculté de Médecine d'Angers-Centre hospitalier universitaire de Nantes (CHU Nantes), Institut d'oncologie/développement Albert Bonniot de Grenoble ( INSERM U823 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -CHU Grenoble-EFS-Institut National de la Santé et de la Recherche Médicale ( INSERM ), University of Oxford [Oxford], Target Discovery Institute (TDI), Nuffield Department of Clinical Medicine, Institut de biologie structurale ( IBS - UMR 5075 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Centre International de Recherche en Infectiologie ( CIRI ), Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-École normale supérieure - Lyon ( ENS Lyon ), Centre for Genomic Regulation [Barcelona] ( CRG ), Universitat Pompeu Fabra [Barcelona]-Centro Nacional de Analisis Genomico [Barcelona] ( CNAG ), Inserm u892, Centre de Recherches en Cancérologie, Nantes, Institut National de la Santé et de la Recherche Médicale (INSERM)-EFS-CHU Grenoble-Université Joseph Fourier - Grenoble 1 (UJF), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)
- Subjects
Adenosine Triphosphatases ,Male ,Proteomics ,histone turnover ,Chromatin Immunoprecipitation ,germ cells ,Genome ,Pax3 ,[ SDV ] Life Sciences [q-bio] ,[SDV]Life Sciences [q-bio] ,FACT ,epidrug ,Acetylation ,Cell Differentiation ,Article ,Chromatin ,Nucleosomes ,DNA-Binding Proteins ,histone chaperone ,ATPases Associated with Diverse Cellular Activities ,Humans ,cancer drug target ,Embryonic Stem Cells ,Cell Proliferation ,Protein Binding - Abstract
International audience; Although the conserved AAA ATPase and bromodomain factor, ATAD2, has been described as a transcriptional co-activator upregulated in many cancers, its function remains poorly understood. Here, using a combination of ChIP-seq, ChIP-proteomics, and RNA-seq experiments in embryonic stem cells where Atad2 is normally highly expressed, we found that Atad2 is an abundant nucleosome-bound protein present on active genes, associated with chromatin remodelling, DNA replication, and DNA repair factors. A structural analysis of its bromodomain and subsequent investigations demonstrate that histone acetylation guides ATAD2 to chromatin, resulting in an overall increase of chromatin accessibility and histone dynamics, which is required for the proper activity of the highly expressed gene fraction of the genome. While in exponentially growing cells Atad2 appears dispensable for cell growth, in differentiating ES cells Atad2 becomes critical in sustaining specific gene expression programmes, controlling proliferation and differentiation. Altogether, this work defines Atad2 as a facilitator of general chromatin-templated activities such as transcription.
- Published
- 2016
8. Loss-of-Function Studies in Mouse Embryonic Stem Cells Using the pHYPER shRNA Plasmid Vector.
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Berlivet, Soizik, Houlard, Martin, and Gérard, Matthieu
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- 2010
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9. Bromodomain-dependent stage-specific male genome programming by Brdt.
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Gaucher, Jonathan, Boussouar, Fayçal, Montellier, Emilie, Curtet, Sandrine, Buchou, Thierry, Bertrand, Sarah, Hery, Patrick, Jounier, Sylvie, Depaux, Arnaud, Vitte, Anne-Laure, Guardiola, Philippe, Pernet, Karin, Debernardi, Alexandra, Lopez, Fabrice, Holota, Hélène, Imbert, Jean, Wolgemuth, Debra J, Gérard, Matthieu, Rousseaux, Sophie, and Khochbin, Saadi
- Subjects
HISTONES ,GENE expression ,GERM cell differentiation ,PROGENITOR cells ,MEIOSIS ,HAPLOIDY ,CHROMATIN - Abstract
Male germ cell differentiation is a highly regulated multistep process initiated by the commitment of progenitor cells into meiosis and characterized by major chromatin reorganizations in haploid spermatids. We report here that a single member of the double bromodomain BET factors, Brdt, is a master regulator of both meiotic divisions and post-meiotic genome repackaging. Upon its activation at the onset of meiosis, Brdt drives and determines the developmental timing of a testis-specific gene expression program. In meiotic and post-meiotic cells, Brdt initiates a genuine histone acetylation-guided programming of the genome by activating essential genes and repressing a 'progenitor cells' gene expression program. At post-meiotic stages, a global chromatin hyperacetylation gives the signal for Brdt's first bromodomain to direct the genome-wide replacement of histones by transition proteins. Brdt is therefore a unique and essential regulator of male germ cell differentiation, which, by using various domains in a developmentally controlled manner, first drives a specific spermatogenic gene expression program, and later controls the tight packaging of the male genome. [ABSTRACT FROM AUTHOR]
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- 2012
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10. CAF-1 Is Essential for Heterochromatin Organization in Pluripotent Embryonic Cells.
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Houlard, Martin, Berlivet, Soizik, Probst, Aline V., Quivy, Jean-Pierre, Héry, Patrick, Almouzni, Geneviève, and Gérard, Matthieu
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EMBRYONIC stem cells ,NUCLEOPROTEINS ,STEM cells ,HETEROCHROMATIN ,CHROMATIN ,PLURIPOTENTIAL theory (Mathematics) - Abstract
During mammalian development, chromatin dynamics and epigenetic marking are important for genome reprogramming. Recent data suggest an important role for the chromatin assembly machinery in this process. To analyze the role of chromatin assembly factor 1 (CAF-1) during pre-implantation development, we generated a mouse line carrying a targeted mutation in the gene encoding its large subunit, p150CAF-1. Loss of p150CAF-1 in homozygous mutants leads to developmental arrest at the 16-cell stage. Absence of p150CAF-1 in these embryos results in severe alterations in the nuclear organization of constitutive heterochromatin. We provide evidence that in wild-type embryos, heterochromatin domains are extensively reorganized between the two-cell and blastocyst stages. In p150CAF-1 mutant 16-cell stage embryos, the altered organization of heterochromatin displays similarities to the structure of heterochromatin in two- to four-cell stage wild-type embryos, suggesting that CAF-1 is required for the maturation of heterochromatin during preimplantation development. In embryonic stem cells, depletion of p150CAF-1 using RNA interference results in the mislocalization, loss of clustering, and decondensation of pericentric heterochromatin domains. Furthermore, loss of CAF-1 in these cells results in the alteration of epigenetic histone methylation marks at the level of pericentric heterochromatin. These alterations of heterochromatin are not found in p150CAF-1-depleted mouse embryonic fibroblasts, which are cells that are already lineage committed, suggesting that CAF-1 is specifically required for heterochromatin organization in pluripotent embryonic cells. Our findings underline the role of the chromatin assembly machinery in controlling the spatial organization and epigenetic marking of the genome in early embryos and embryonic stem cells. INSET: Synopsis. [ABSTRACT FROM AUTHOR]
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- 2006
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11. Disruption of the mouse necdin gene results in early post-natal lethality.
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Gérard, Matthieu, Hernandez, Lidia, Wevrick, Rachel, and Stewart, Colin L.
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PRADER-Willi syndrome , *NEUROBEHAVIORAL disorders , *INFANT diseases - Abstract
Prader-Willi syndrome (PWS) is a neurobehavioural disorder characterized by neonatal respiratory depression, hypotonia and failure to thrive in infancy, followed by hyperphagia and obesity among other symptoms. PWS is caused by the loss of one or more paternally expressed genes on chromosome 15q11-q13, which can be due to gene deletions, maternal uniparental disomy or mutations disrupting the imprinting mechanism. Imprinted genes mapped to this region include SNRPN (refs 3,4), ZNF127 (ref. 5), IPW (ref. 6) and NDN (which encodes the DNA-binding protein necdin; refs 7-10). The mouse homologues of these genes map to mouse chromosome 7 in a region syntenic with human chromosome 15q11-q13 (refs 7,11). Imprinting of the human genes is under the control of an imprinting center (lC), a long-range, cis-acting element located in the 5' region of SNRPN (ref. 12). A related control element was isolated in the mouse Snrpn genomic region which, when deleted on the paternally inherited chromosome, resulted in the loss of expression of all four genes and early post-natal lethality. To determine the possible contribution of Ndn to the PWS phenotype, we generated Ndn mutant mice. Heterozygous mice inheriting the mutated maternal allele were indistinguishable from their wild-type littermates. Mice carrying a paternally inherited Ndn deletion allele demonstrated early post-natal lethality. This is the first example of a single gene being responsible for phenotypes associated with PWS. [ABSTRACT FROM AUTHOR]
- Published
- 1999
12. Nut Directs p300-Dependent, Genome-Wide H4 Hyperacetylation in Male Germ Cells.
- Author
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Shiota, Hitoshi, Barral, Sophie, Buchou, Thierry, Tan, Minjia, Couté, Yohann, Charbonnier, Guillaume, Reynoird, Nicolas, Boussouar, Fayçal, Gérard, Matthieu, Zhu, Mingrui, Bargier, Lisa, Puthier, Denis, Chuffart, Florent, Bourova-Flin, Ekaterina, Picaud, Sarah, Filippakopoulos, Panagis, Goudarzi, Afsaneh, Ibrahim, Ziad, Panne, Daniel, and Rousseaux, Sophie
- Abstract
Summary Nuclear protein in testis (Nut) is a universal oncogenic driver in the highly aggressive NUT midline carcinoma, whose physiological function in male germ cells has been unclear. Here we show that expression of Nut is normally restricted to post-meiotic spermatogenic cells, where its presence triggers p300-dependent genome-wide histone H4 hyperacetylation, which is essential for the completion of histone-to-protamine exchange. Accordingly, the inactivation of Nut induces male sterility with spermatogenesis arrest at the histone-removal stage. Nut uses p300 and/or CBP to enhance acetylation of H4 at both K5 and K8, providing binding sites for the first bromodomain of Brdt, the testis-specific member of the BET family, which subsequently mediates genome-wide histone removal. Altogether, our data reveal the detailed molecular basis of the global histone hyperacetylation wave, which occurs before the final compaction of the male genome. Graphical Abstract Highlights • Nut is a post-meiotically expressed gene that is critical for male fertility • Nut recruits p300 and/or CBP to enhance histone H4K5 and H4K8 acetylation • Nut-mediated histone hyperacetylation is required for histone-to-protamine transition A transcription-independent histone hyperacetylation is associated with near-total histone replacement during mouse spermatogenesis. Shiota et al. show the oncogenic factor Nut is expressed in post-meiotic male germ cells, where it recruits p300 and/or CBP and enhances histone H4K5 and H4K8 acetylation, leading to histone-to-protamine replacement. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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13. 2007-2017, a Decade of Functional Analysis of Mammalian Genomes.
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GÉRARD, MATTHIEU
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GENOMICS , *ACQUISITION of data , *FUNCTIONAL analysis - Abstract
The article focuses on the functional analysis of the genomics which is used to develop protocols and collect data for the fields.
- Published
- 2017
14. Purification of the upstream element factor of the Adenovirus-2 major late promoter from HeLa and yeast by sequence-specific DNA affinity chromatography
- Author
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Moncollin, Vincent, Gerard, Matthieu, and Egly, Jean-Marc
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- 1990
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15. Histone H3 trimethylation at lysine 36 is associated with constitutive and facultative heterochromatin.
- Author
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Chantalat, Sophie, Depaux, Arnaud, Héry, Patrick, Barral, Sophie, Thuret, Jean-Yves, Dimitrov, Stefan, and Gérard, Matthieu
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- *
HISTONES , *GENE silencing , *HETEROCHROMATIN , *LYSINE , *EMBRYONIC stem cell research , *LABORATORY mice , *GENOMES - Abstract
The mammalian genome contains numerous regions known as facultative heterochromatin, which contribute to transcriptional silencing during development and cell differentiation. We have analyzed the pattern of histone modifications associated with facultative heterochromatin within the mouse imprinted Snurf-Snrpn cluster, which is homologous to the human Prader-Willi syndrome genomic region. We show here that the maternally inherited Snurf-Snrpn 3-Mb region, which is silenced by a potent transcription repressive mechanism, is uniformly enriched in histone methylation marks usually found in constitutive heterochromatin, such as H4K20me3, H3K9me3, and H3K79me3. Strikingly, we found that trimethylated histone H3 at lysine 36 (H3K36me3), which was previously identified as a hallmark of actively transcribed regions, is deposited onto the silenced, maternally contributed 3-Mb imprinted region. We show that H3K36me3 deposition within this large heterochromatin domain does not correlate with transcription events, suggesting the existence of an alternative pathway for the deposition of this histone modification. In addition, we demonstrate that H3K36me3 is markedly enriched at the level of pericentromeric heterochromatin in mouse embryonic stem cells and fibroblasts. This result indicates that H3K36me3 is associated with both facultative and constitutive heterochromatin. Our data suggest that H3K36me3 function is not restricted to actively transcribed regions only and may contribute to the composition of heterochromatin, in combination with other histone modifications. [ABSTRACT FROM AUTHOR]
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- 2011
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16. Regulation of RNA Polymerase III Transcription by Maf1 in Mammalian Cells
- Author
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Goodfellow, Sarah J., Graham, Emma L., Kantidakis, Theodoros, Marshall, Lynne, Coppins, Beverly A., Oficjalska-Pham, Danuta, Gérard, Matthieu, Lefebvre, Olivier, and White, Robert J.
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RNA , *RNA polymerases , *SACCHAROMYCES cerevisiae , *FIBROBLASTS - Abstract
Abstract: RNA polymerase (pol) III produces essential components of the biosynthetic machinery; therefore, its output is tightly coupled with the rate of cell growth and proliferation. In Saccharomyces cerevisiae, Maf1 is an essential mediator of pol III repression in response to starvation. We demonstrate that a Maf1 ortholog is also used to restrain pol III activity in mouse and human cells. Mammalian Maf1 represses pol III transcription in vitro and in transfected fibroblasts. Furthermore, genetic deletion of Maf1 elevates pol III transcript expression, thus confirming the role of endogenous Maf1 as an inhibitor of mammalian pol III output. Maf1 is detected at chromosomal pol III templates in rodent and human cells. It interacts with pol III as well as its associated initiation factor TFIIIB and is phosphorylated in a serum-sensitive manner in vivo. These aspects of Maf1 function have been conserved between yeast and mammals and are therefore likely to be of fundamental importance in controlling pol III transcriptional activity. [Copyright &y& Elsevier]
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- 2008
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17. Histone Variant H2A.L.2 Guides Transition Protein-Dependent Protamine Assembly in Male Germ Cells.
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Barral, Sophie, Morozumi, Yuichi, Tanaka, Hiroki, Montellier, Emilie, Govin, Jérôme, de Dieuleveult, Maud, Charbonnier, Guillaume, Couté, Yohann, Puthier, Denis, Buchou, Thierry, Boussouar, Fayçal, Urahama, Takashi, Fenaille, François, Curtet, Sandrine, Héry, Patrick, Fernandez-Nunez, Nicolas, Shiota, Hitoshi, Gérard, Matthieu, Rousseaux, Sophie, and Kurumizaka, Hitoshi
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HISTONES , *PROTAMINES , *GERM cells , *CHROMATIN , *SPERMATOZOA - Abstract
Summary Histone replacement by transition proteins (TPs) and protamines (Prms) constitutes an essential step for the successful production of functional male gametes, yet nothing is known on the underlying functional interplay between histones, TPs, and Prms. Here, by studying spermatogenesis in the absence of a spermatid-specific histone variant, H2A.L.2, we discover a fundamental mechanism involved in the transformation of nucleosomes into nucleoprotamines. H2A.L.2 is synthesized at the same time as TPs and enables their loading onto the nucleosomes. TPs do not displace histones but rather drive the recruitment and processing of Prms, which are themselves responsible for histone eviction. Altogether, the incorporation of H2A.L.2 initiates and orchestrates a series of successive transitional states that ultimately shift to the fully compacted genome of the mature spermatozoa. Hence, the current view of histone-to-nucleoprotamine transition should be revisited and include an additional step with H2A.L.2 assembly prior to the action of TPs and Prms. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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18. Corrigendum to “Regulation of RNA Polymerase III Transcription by Maf1 in Mammalian Cells” [J. Mol. Biol. 378(3) (2008) 481–491]
- Author
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Goodfellow, Sarah J., Graham, Emma L., Kantidakis, Theodoros, Marshall, Lynne, Coppins, Beverly A., Oficjalska-Pham, Danuta, Gérard, Matthieu, Lefebvre, Olivier, and White, Robert J.
- Published
- 2013
- Full Text
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19. cBAF generates subnucleosomes that expand OCT4 binding and function beyond DNA motifs at enhancers.
- Author
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Nocente MC, Mesihovic Karamitsos A, Drouineau E, Soleil M, Albawardi W, Dulary C, Ribierre F, Picaud H, Alibert O, Acker J, Kervella M, Aude JC, Gilbert N, Ochsenbein F, Chantalat S, and Gérard M
- Abstract
The canonical BRG/BRM-associated factor (cBAF) complex is essential for chromatin opening at enhancers in mammalian cells. However, the nature of the open chromatin remains unclear. Here, we show that, in addition to producing histone-free DNA, cBAF generates stable hemisome-like subnucleosomal particles containing the four core histones associated with 50-80 bp of DNA. Our genome-wide analysis indicates that cBAF makes these particles by targeting and splitting fragile nucleosomes. In mouse embryonic stem cells, these subnucleosomes become an in vivo binding substrate for the master transcription factor OCT4 independently of the presence of OCT4 DNA motifs. At enhancers, the OCT4-subnucleosome interaction increases OCT4 occupancy and amplifies the genomic interval bound by OCT4 by up to one order of magnitude compared to the region occupied on histone-free DNA. We propose that cBAF-dependent subnucleosomes orchestrate a molecular mechanism that projects OCT4 function in chromatin opening beyond its DNA motifs., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)
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- 2024
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20. Efficient Depletion of Essential Gene Products for Loss-of-Function Studies in Embryonic Stem Cells.
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Berlivet S, Hmitou I, Picaud H, and Gérard M
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- Animals, Electroporation, Mice, Plasmids genetics, RNA Interference, RNA, Small Interfering genetics, Transfection, Embryonic Stem Cells metabolism, Genes, Essential, Loss of Function Mutation
- Abstract
The development of the CRISPR/Cas9 technology has provided powerful methods to target genetic alterations. However, investigating the function of genes essential for cell survival remains problematic, because genetic ablation of these genes results in cell death. As a consequence, cells recombined at the targeted gene and fully depleted of the gene product cannot be obtained. RNA interference is well suited for the study of essential genes, but this approach often results in a partial depletion of the targeted gene product, which can lead to misinterpretations. We previously developed the pHYPER shRNA vector, a high efficiency RNA interference vector, which is based on a 2.5-kb mouse genomic fragment encompassing the H1 gene. We provide here a pHYPER-based protocol optimized to study the function of essential gene products in mouse embryonic stem cells.
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- 2017
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21. Atad2 is a generalist facilitator of chromatin dynamics in embryonic stem cells.
- Author
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Morozumi Y, Boussouar F, Tan M, Chaikuad A, Jamshidikia M, Colak G, He H, Nie L, Petosa C, de Dieuleveult M, Curtet S, Vitte AL, Rabatel C, Debernardi A, Cosset FL, Verhoeyen E, Emadali A, Schweifer N, Gianni D, Gut M, Guardiola P, Rousseaux S, Gérard M, Knapp S, Zhao Y, and Khochbin S
- Subjects
- ATPases Associated with Diverse Cellular Activities, Acetylation, Cell Differentiation, Cell Proliferation, Chromatin Immunoprecipitation, Embryonic Stem Cells cytology, Genome, Germ Cells metabolism, Humans, Male, Nucleosomes metabolism, Protein Binding, Proteomics, Adenosine Triphosphatases metabolism, Chromatin metabolism, DNA-Binding Proteins metabolism, Embryonic Stem Cells metabolism
- Abstract
Although the conserved AAA ATPase and bromodomain factor, ATAD2, has been described as a transcriptional co-activator upregulated in many cancers, its function remains poorly understood. Here, using a combination of ChIP-seq, ChIP-proteomics, and RNA-seq experiments in embryonic stem cells where Atad2 is normally highly expressed, we found that Atad2 is an abundant nucleosome-bound protein present on active genes, associated with chromatin remodelling, DNA replication, and DNA repair factors. A structural analysis of its bromodomain and subsequent investigations demonstrate that histone acetylation guides ATAD2 to chromatin, resulting in an overall increase of chromatin accessibility and histone dynamics, which is required for the proper activity of the highly expressed gene fraction of the genome. While in exponentially growing cells Atad2 appears dispensable for cell growth, in differentiating ES cells Atad2 becomes critical in sustaining specific gene expression programmes, controlling proliferation and differentiation. Altogether, this work defines Atad2 as a facilitator of general chromatin-templated activities such as transcription., (© The Author (2015). Published by Oxford University Press on behalf of Journal of Molecular Cell Biology, IBCB, SIBS, CAS.)
- Published
- 2016
- Full Text
- View/download PDF
22. Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B.
- Author
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Montellier E, Boussouar F, Rousseaux S, Zhang K, Buchou T, Fenaille F, Shiota H, Debernardi A, Héry P, Curtet S, Jamshidikia M, Barral S, Holota H, Bergon A, Lopez F, Guardiola P, Pernet K, Imbert J, Petosa C, Tan M, Zhao Y, Gérard M, and Khochbin S
- Subjects
- Animals, Epigenesis, Genetic, Female, Fertilization physiology, Gene Expression Regulation, Developmental, Genome, Histones genetics, Male, Meiosis, Mice, Nucleosomes, Spermatogenesis genetics, Testis metabolism, Chromatin metabolism, Histones metabolism, Protamines metabolism
- Abstract
The conversion of male germ cell chromatin to a nucleoprotamine structure is fundamental to the life cycle, yet the underlying molecular details remain obscure. Here we show that an essential step is the genome-wide incorporation of TH2B, a histone H2B variant of hitherto unknown function. Using mouse models in which TH2B is depleted or C-terminally modified, we show that TH2B directs the final transformation of dissociating nucleosomes into protamine-packed structures. Depletion of TH2B induces compensatory mechanisms that permit histone removal by up-regulating H2B and programming nucleosome instability through targeted histone modifications, including lysine crotonylation and arginine methylation. Furthermore, after fertilization, TH2B reassembles onto the male genome during protamine-to-histone exchange. Thus, TH2B is a unique histone variant that plays a key role in the histone-to-protamine packing of the male genome and guides genome-wide chromatin transitions that both precede and follow transmission of the male genome to the egg.
- Published
- 2013
- Full Text
- View/download PDF
23. Loss-of-function studies in mouse embryonic stem cells using the pHYPER shRNA plasmid vector.
- Author
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Berlivet S, Houlard M, and Gérard M
- Subjects
- Animals, Blotting, Western, Cells, Cultured, Chromatin Assembly Factor-1 genetics, Chromatin Assembly Factor-1 metabolism, Electrophoresis, Polyacrylamide Gel, Mice, Promoter Regions, Genetic genetics, RNA, Small Interfering genetics, Embryonic Stem Cells metabolism, Genetic Vectors genetics, Plasmids genetics, RNA, Small Interfering physiology
- Abstract
RNA interference is widely used for loss-of-function studies in mammalian cells. As an alternative to the transfection of small RNAs, plasmid vectors have been developed to express short hairpin RNAs (shRNAs). We engineered the pHYPER shRNA vector, which is based on a 2.5-kb mouse genomic fragment encompassing the H1 gene. We have previously shown that this shRNA vector is highly efficient for both transient transfection studies in embryonic stem (ES) cells and generation of stable ES cell lines. Following ES cell transfection, the H1 promoter of pHYPER is recognized by the RNA polymerase III machinery, which directs the transcription of the shRNA. We provide here detailed protocols that explain how to optimize the use of pHYPER in ES cells.
- Published
- 2010
- Full Text
- View/download PDF
24. pHYPER, a shRNA vector for high-efficiency RNA interference in embryonic stem cells.
- Author
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Berlivet S, Guiraud V, Houlard M, and Gérard M
- Subjects
- Animals, Cell Line, Crosses, Genetic, Embryonic Stem Cells cytology, Mice, Mice, Inbred C3H, Mice, Transgenic, Embryonic Stem Cells physiology, Genetic Vectors, RNA Interference, RNA, Small Interfering genetics
- Abstract
RNA interference (RNAi) is a powerful method to generate loss-of-function phenotypes. Plasmid vectors with RNA polymerase III promoters have been developed to express short hairpin RNAs (shRNAs) in mammalian cells. In order to optimize the efficiency of these vectors in embryonic stem (ES) cells, we have constructed and tested several plasmids, based on the H1 promoter; that direct the expression of shRNAs. The original pSUPER vector was used as a reference in this study. This vector drives the expression of shRNAs from a basic 0.2-kb H1 promoter; which exhibits a variable expression when integrated into the genome of ES cells. We used a 2.5-kb mouse genomic fragment containing the H1 promoter to construct a new H1 shRNA vector pHYPER. A comparison of this vector with the basic 0.2-kb H1 vector showed that pHYPER directs the synthesis of higher amounts of shRNAs. Using epifluorescence and fluorescent-activated cell sorting (FACS) analysis, we demonstrated that pHYPER is 4-fold more active than the 0.2-kb H1-based vector after integration into the genome of mouse ES cells. We provide a new, improved H1 shRNA vector that is optimized for both transient transfection studies and the generation of stable ES cell lines.
- Published
- 2007
- Full Text
- View/download PDF
25. Absence of Ndn, encoding the Prader-Willi syndrome-deleted gene necdin, results in congenital deficiency of central respiratory drive in neonatal mice.
- Author
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Ren J, Lee S, Pagliardini S, Gérard M, Stewart CL, Greer JJ, and Wevrick R
- Subjects
- Animals, Animals, Newborn, Biological Clocks genetics, Brain Stem pathology, Brain Stem physiopathology, Diaphragm physiopathology, Electromyography, In Vitro Techniques, Membrane Potentials genetics, Mice, Mice, Neurologic Mutants, Nerve Tissue Proteins genetics, Neurons metabolism, Neurons pathology, Nuclear Proteins genetics, Patch-Clamp Techniques, RNA, Messenger biosynthesis, Respiratory Center embryology, Respiratory Center pathology, Respiratory Insufficiency pathology, Respiratory Insufficiency physiopathology, Spinal Cord pathology, Spinal Cord physiopathology, Nerve Tissue Proteins deficiency, Nuclear Proteins deficiency, Prader-Willi Syndrome genetics, Respiratory Center physiopathology, Respiratory Insufficiency congenital, Respiratory Insufficiency genetics
- Abstract
necdin (Ndn) is one of a cluster of genes deleted in the neurodevelopmental disorder Prader-Willi syndrome. necdin is upregulated during neuronal differentiation and is thought to play a role in cell cycle arrest in terminally differentiated neurons. Most necdin-deficient Ndn(tm2Stw) mutant pups carrying a targeted replacement of Ndn with a lacZ reporter gene die in the neonatal period of apparent respiratory insufficiency. We now demonstrate that the defect can be explained by abnormal neuronal activity within the putative respiratory rhythm-generating center, the pre-Bötzinger complex. Specifically, the rhythm is unstable with prolonged periods of depression of respiratory rhythmogenesis. These observations suggest that the developing respiratory center is particularly sensitive to loss of necdin activity and may reflect abnormalities of respiratory rhythm-generating neurons or conditioning neuromodulatory drive. We propose that necdin deficiency may contribute to observed respiratory abnormalities in individuals with Prader-Willi syndrome through a similar suppression of central respiratory drive.
- Published
- 2003
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