Dynamique de la Chromatine

Publications de l’équipe

Année de publication : 2015

Casey E Romanoski, Christopher K Glass, Hendrik G Stunnenberg, Laurence Wilson, Genevieve Almouzni (2015 Feb 20)

Epigenomics: Roadmap for regulation.

Nature : 314-6 : DOI : 10.1038/518314a En savoir plus
Résumé

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Nicolas Richet, Danni Liu, Pierre Legrand, Christophe Velours, Armelle Corpet, Albane Gaubert, May Bakail, Gwenaelle Moal-Raisin, Raphael Guerois, Christel Compper, Arthur Besle, Berengère Guichard, Genevieve Almouzni, Françoise Ochsenbein (2015 Jan 23)

Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork.

Nucleic acids research : 1905-17 : DOI : 10.1093/nar/gkv021 En savoir plus
Résumé

MCM2 is a subunit of the replicative helicase machinery shown to interact with histones H3 and H4 during the replication process through its N-terminal domain. During replication, this interaction has been proposed to assist disassembly and assembly of nucleosomes on DNA. However, how this interaction participates in crosstalk with histone chaperones at the replication fork remains to be elucidated. Here, we solved the crystal structure of the ternary complex between the histone-binding domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4 assemble as a tetramer in the crystal structure, but MCM2 interacts only with a single molecule of H3-H4. The latter interaction exploits binding surfaces that contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome core particle. Upon binding of the ternary complex with the histone chaperone ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis of the quaternary complex together with structural modeling support that ASF1 and MCM2 could form a chaperoning module for histones H3 and H4 protecting them from promiscuous interactions. This suggests an additional function for MCM2 outside its helicase function as a proper histone chaperone connected to the replication pathway.

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Année de publication : 2014

Yasuhiro Arimura, Kazuyoshi Shirayama, Naoki Horikoshi, Risa Fujita, Hiroyuki Taguchi, Wataru Kagawa, Tatsuo Fukagawa, Geneviève Almouzni, Hitoshi Kurumizaka (2014 Oct 30)

Crystal structure and stable property of the cancer-associated heterotypic nucleosome containing CENP-A and H3.3.

Scientific reports : 7115 : DOI : 10.1038/srep07115 En savoir plus
Résumé

The centromere-specific histone H3 variant, CENP-A, is overexpressed in particular aggressive cancer cells, where it can be mislocalized ectopically in the form of heterotypic nucleosomes containing H3.3. In the present study, we report the crystal structure of the heterotypic CENP-A/H3.3 particle and reveal its « hybrid structure », in which the physical characteristics of CENP-A and H3.3 are conserved independently within the same particle. The CENP-A/H3.3 nucleosome forms an unexpectedly stable structure as compared to the CENP-A nucleosome, and allows the binding of the essential centromeric protein, CENP-C, which is ectopically mislocalized in the chromosomes of CENP-A overexpressing cells.

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Dan Filipescu, Sebastian Müller, Geneviève Almouzni (2014 Oct 8)

Histone H3 variants and their chaperones during development and disease: contributing to epigenetic control.

Annual review of cell and developmental biology : 615-46 : DOI : 10.1146/annurev-cellbio-100913-013311 En savoir plus
Résumé

Within the nucleus, the interplay between lineage-specific transcription factors and chromatin dynamics defines cellular identity. Control of this interplay is necessary to properly balance stability and plasticity during the development and entire life span of multicellular organisms. Here, we present our current knowledge of the contribution of histone H3 variants to chromatin dynamics during development. We review the network of histone chaperones that governs their deposition timing and sites of incorporation and highlight how their distinct distribution impacts genome organization and function. We integrate the importance of H3 variants in the context of nuclear reprogramming and cell differentiation, and, using the centromere as a paradigm, we describe a case in which the identity of a given genomic locus is propagated across different cell types. Finally, we compare development to changes in stress and disease. Both physiological and pathological settings underline the importance of H3 dynamics for genome and chromatin integrity.

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Zachary A Gurard-Levin, Geneviève Almouzni (2014 Sep 4)

Histone modifications and a choice of variant: a language that helps the genome express itself.

F1000prime reports : 76 : DOI : 10.12703/P6-76 En savoir plus
Résumé

Covalent post-translational modifications on histones impact chromatin structure and function. Their misfunction, along with perturbations or mutations in genes that regulate their dynamic status, has been observed in several diseases. Thus, targeting histone modifications represents attractive opportunities for therapeutic intervention and biomarker discovery. The best approach to address this challenge is to paint a comprehensive picture integrating the growing number of modifications on individual residues and their combinatorial association, the corresponding modifying enzymes, and effector proteins that bind modifications. Furthermore, how they are imposed in a distinct manner during the cell cycle and on specific histone variants are important dimensions to consider. Firstly, this report highlights innovative technologies used to characterize histone modifications, and the corresponding enzymes and effector proteins. Secondly, we examine the recent progress made in understanding the dynamics and maintenance of histone modifications on distinct variants. We also discuss their roles as potential carriers of epigenetic information. Finally, we provide examples of initiatives to exploit histone modifications in cancer management, with the potential for new therapeutic opportunities.

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Kelly Romeo, Yann Louault, Sylvain Cantaloube, Isabelle Loiodice, Geneviève Almouzni, Jean-Pierre Quivy (2014 Jul 31)

The SENP7 SUMO-Protease Presents a Module of Two HP1 Interaction Motifs that Locks HP1 Protein at Pericentric Heterochromatin.

Cell reports : DOI : S2211-1247(15)00005-4 En savoir plus
Résumé

HP1 enrichment at pericentric heterochromatin is essential for proper chromosome segregation. While H3K9me3 is thought to be a major contributor to HP1 enrichment at pericentric domains, in mouse cells, the SUMO-protease SENP7 is required in addition to H3K9me3. How this is achieved remains elusive. Here, we find that loss of SENP7 leads to an increased time spent in mitosis. Furthermore, we reveal that a short module comprising two consecutive HP1 interaction motifs on SENP7 is the determinant for HP1 enrichment and acts by restricting HP1 mobility at pericentric domains. We propose a mechanism for maintenance of HP1 enrichment in which this module functions on top of H3K9me3 to lock contiguous HP1 molecules already docked on H3K9me3-modified nucleosomes. H3K9me3 would thus promote HP1 enrichment only if a locking system is in place. This mechanism may apply to other nuclear domains to contribute to the control of genome plasticity and integrity.

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Roderick J O'Sullivan, Genevieve Almouzni (2014 Jul 2)

Assembly of telomeric chromatin to create ALTernative endings.

Trends in cell biology : 675-85 : DOI : 10.1016/j.tcb.2014.07.007 En savoir plus
Résumé

Circumvention of the telomere length-dependent mechanisms that control the upper boundaries of cellular proliferation is necessary for the unlimited growth of cancer. Most cancer cells achieve cellular immortality by up-regulating the expression of telomerase to extend and maintain their telomere length. However, a small but significant number of cancers do so via the exchange of telomeric DNA between chromosomes in a pathway termed alternative lengthening of telomeres, or ALT. Although it remains to be clarified why a cell chooses the ALT pathway and how ALT is initiated, recently identified mutations in factors that shape the chromatin and epigenetic landscape of ALT telomeres are shedding light on these mechanisms. In this review, we examine these recent findings and integrate them into the current models of the ALT mechanism.

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Zachary A Gurard-Levin, Jean-Pierre Quivy, Geneviève Almouzni (2014 Jun 7)

Histone chaperones: assisting histone traffic and nucleosome dynamics.

Annual review of biochemistry : 487-517 : DOI : 10.1146/annurev-biochem-060713-035536 En savoir plus
Résumé

The functional organization of eukaryotic DNA into chromatin uses histones as components of its building block, the nucleosome. Histone chaperones, which are proteins that escort histones throughout their cellular life, are key actors in all facets of histone metabolism; they regulate the supply and dynamics of histones at chromatin for its assembly and disassembly. Histone chaperones can also participate in the distribution of histone variants, thereby defining distinct chromatin landscapes of importance for genome function, stability, and cell identity. Here, we discuss our current knowledge of the known histone chaperones and their histone partners, focusing on histone H3 and its variants. We then place them into an escort network that distributes these histones in various deposition pathways. Through their distinct interfaces, we show how they affect dynamics during DNA replication, DNA damage, and transcription, and how they maintain genome integrity. Finally, we discuss the importance of histone chaperones during development and describe how misregulation of the histone flow can link to disease.

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Ekaterina Boyarchuk, Dan Filipescu, Isabelle Vassias, Sylvain Cantaloube, Geneviève Almouzni (2014 Jun 6)

The histone variant composition of centromeres is controlled by the pericentric heterochromatin state during the cell cycle.

Journal of cell science : 3347-59 : DOI : 10.1242/jcs.148189 En savoir plus
Résumé

Correct chromosome segregation requires a unique chromatin environment at centromeres and in their vicinity. Here, we address how the deposition of canonical H2A and H2A.Z histone variants is controlled at pericentric heterochromatin (PHC). Whereas in euchromatin newly synthesized H2A and H2A.Z are deposited throughout the cell cycle, we reveal two discrete waves of deposition at PHC – during mid to late S phase in a replication-dependent manner for H2A and during G1 phase for H2A.Z. This G1 cell cycle restriction is lost when heterochromatin features are altered, leading to the accumulation of H2A.Z at the domain. Interestingly, compromising PHC integrity also impacts upon neighboring centric chromatin, increasing the amount of centromeric CENP-A without changing the timing of its deposition. We conclude that the higher-order chromatin structure at the pericentric domain influences dynamics at the nucleosomal level within centromeric chromatin. The two different modes of rearrangement of the PHC during the cell cycle provide distinct opportunities to replenish one or the other H2A variant, highlighting PHC integrity as a potential signal to regulate the deposition timing and stoichiometry of histone variants at the centromere.

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Catherine Dehainault, Alexandra Garancher, Laurent Castéra, Nathalie Cassoux, Isabelle Aerts, François Doz, Laurence Desjardins, Livia Lumbroso, Rocío Montes de Oca, Geneviève Almouzni, Dominique Stoppa-Lyonnet, Celio Pouponnot, Marion Gauthier-Villars, Claude Houdayer (2014 May 23)

The survival gene MED4 explains low penetrance retinoblastoma in patients with large RB1 deletion.

Human molecular genetics : 5243-50 : DOI : 10.1093/hmg/ddu245 En savoir plus
Résumé

Retinoblastoma is a non-hereditary as well as an inherited pediatric tumor of the developing retina resulting from the inactivation of both copies of the RB1 tumor suppressor gene. Familial retinoblastoma is a highly penetrant genetic disease that usually develops by carrying germline mutations that inactivate one allele of the RB1 gene, leading to multiple retinoblastomas. However, large and complete germline RB1 deletions are associated with low or no tumor risk for reasons that remain unknown. In this study, we define a minimal genomic region associated with this low penetrance. This region encompasses few genes including MED4 a subunit of the mediator complex. We further show that retinoblastoma RB1 -/- cells cannot survive in the absence of MED4, both in vitro and in orthotopic xenograft models in vivo, therefore identifying MED4 as a survival gene in retinoblastoma. We propose that the contiguous loss of the adjacent retinoblastoma gene, MED4, explains the low penetrance in patients with large deletions that include both RB1 and MED4. Our findings also point to another synthetic lethal target in tumors with inactivated RB1 and highlight the importance of collateral damage in carcinogenesis.

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Sebastian Müller, Rocio Montes de Oca, Nicolas Lacoste, Florent Dingli, Damarys Loew, Geneviève Almouzni (2014 Apr 8)

Phosphorylation and DNA binding of HJURP determine its centromeric recruitment and function in CenH3(CENP-A) loading.

Cell reports : 190-203 : DOI : 10.1016/j.celrep.2014.06.002 En savoir plus
Résumé

Centromeres, epigenetically defined by the presence of the histone H3 variant CenH3, are essential for ensuring proper chromosome segregation. In mammals, centromeric CenH3(CENP-A) deposition requires its dedicated chaperone HJURP and occurs during telophase/early G1. We find that the cell-cycle-dependent recruitment of HJURP to centromeres depends on its timely phosphorylation controlled via cyclin-dependent kinases. A nonphosphorylatable HJURP mutant localizes prematurely to centromeres in S and G2 phase. This unregulated targeting causes a premature loading of CenH3(CENP-A) at centromeres, and cell-cycle delays ensue. Once recruited to centromeres, HJURP functions to promote CenH3(CENP-A) deposition by a mechanism involving a unique DNA-binding domain. With our findings, we propose a model wherein (1) the phosphorylation state of HJURP controls its centromeric recruitment in a cell-cycle-dependent manner, and (2) HJURP binding to DNA is a mechanistic determinant in CenH3(CENP-A) loading.

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Paolo Beuzer, Jean-Pierre Quivy, Geneviève Almouzni (2014 Mar 25)

Establishment of a replication fork barrier following induction of DNA binding in mammalian cells.

Cell cycle (Georgetown, Tex.) : 1607-16 : DOI : 10.4161/cc.28627 En savoir plus
Résumé

Understanding the mechanisms that lead to replication fork blocks (RFB) and the means to bypass them is important given the threat that they represent for genome stability if inappropriately handled. Here, to study this issue in mammals, we use integrated arrays of the LacO and/or TetO as a tractable system to follow in time a process in an individual cell and at a single locus. Importantly, we show that induction of the binding by LacI and TetR proteins, and not the presence of the repeats, is key to form the RFB. We find that the binding of the proteins to the arrays during replication causes a prolonged persistence of replication foci at the site. This, in turn, induces a local DNA damage repair (DDR) response, with the recruitment of proteins involved in double-strand break (DSB) repair such as TOPBP1 and 53BP1, and the phosphorylation of H2AX. Furthermore, the appearance of micronuclei and DNA bridges after mitosis is consistent with an incomplete replication. We discuss how the many DNA binding proteins encountered during replication can be dealt with and the consequences of incomplete replication. Future studies exploiting this type of system should help analyze how an RFB, along with bypass mechanisms, are controlled in order to maintain genome integrity.

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Geneviève Almouzni, Lucia Altucci, Bruno Amati, Neil Ashley, David Baulcombe, Nathalie Beaujean, Christoph Bock, Erik Bongcam-Rudloff, Jean Bousquet, Sigurd Braun, Brigitte Bressac-de Paillerets, Marion Bussemakers, Laura Clarke, Ana Conesa, Xavier Estivill, Alireza Fazeli, Neža Grgurević, Ivo Gut, Bastiaan T Heijmans, Sylvie Hermouet, Jeanine Houwing-Duistermaat, Ilaria Iacobucci, Janez Ilaš, Raju Kandimalla, Susanne Krauss-Etschmann, Paul Lasko, Sören Lehmann, Anders Lindroth, Gregor Majdič, Eric Marcotte, Giovanni Martinelli, Nadine Martinet, Eric Meyer, Cristina Miceli, Ken Mills, Maria Moreno-Villanueva, Ghislaine Morvan, Dörthe Nickel, Beate Niesler, Mariusz Nowacki, Jacek Nowak, Stephan Ossowski, Mattia Pelizzola, Roland Pochet, Uroš Potočnik, Magdalena Radwanska, Jeroen Raes, Magnus Rattray, Mark D Robinson, Bernard Roelen, Sascha Sauer, Dieter Schinzer, Eline Slagboom, Tim Spector, Hendrik G Stunnenberg, Ekaterini Tiligada, Maria-Elena Torres-Padilla, Roula Tsonaka, Ann Van Soom, Melita Vidaković, Martin Widschwendter (2014 Feb 20)

Relationship between genome and epigenome–challenges and requirements for future research.

BMC genomics : 487 : DOI : 10.1186/1471-2164-15-487 En savoir plus
Résumé

Understanding the links between genetic, epigenetic and non-genetic factors throughout the lifespan and across generations and their role in disease susceptibility and disease progression offer entirely new avenues and solutions to major problems in our society. To overcome the numerous challenges, we have come up with nine major conclusions to set the vision for future policies and research agendas at the European level.

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Salomé Adam, Sophie E Polo, Geneviève Almouzni (2014 Feb 10)

How to restore chromatin structure and function in response to DNA damage–let the chaperones play: delivered on 9 July 2013 at the 38th FEBS Congress in St Petersburg, Russia.

The FEBS journal : 2315-23 : DOI : 10.1111/febs.12793 En savoir plus
Résumé

Histone deposition onto DNA assisted by specific chaperones forms the chromatin basic unit and serves to package the genome within the cell nucleus. The resulting chromatin organization, often referred to as the epigenome, contributes to a unique transcriptional program that defines cell identity. Importantly, during cellular life, substantial alterations in chromatin structure may arise due to cell stress, including DNA damage, which not only challenges the integrity of the genome but also threatens the epigenome. Considerable efforts have been made to decipher chromatin dynamics in response to genotoxic stress, and to assess how it affects both genome and epigenome stability. Here, we review recent advances in understanding the mechanisms of DNA damage-induced chromatin plasticity in mammalian cells. We focus specifically on the dynamics of histone H3 variants in response to UV irradiation, and highlight the role of their dedicated chaperones in restoring both chromatin structure and function. Finally, we discuss how, in addition to restoring chromatin integrity, the cellular networks that signal and repair DNA damage may also provide a window of opportunity for modulating the information conveyed by chromatin.

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Sebastian Müller, Geneviève Almouzni (2014 Jan 1)

A network of players in H3 histone variant deposition and maintenance at centromeres.

Biochimica et biophysica acta : 241-50 : DOI : 10.1016/j.bbagrm.2013.11.008 En savoir plus
Résumé

Centromeres are key chromosomal landmarks important for chromosome segregation and are characterized by distinct chromatin features. The centromeric histone H3 variant, referred to as CENP-A or CenH3(CENP-A) in mammals, has emerged as a key determinant for centromeric structure, function and epigenetic inheritance. To regulate the correct incorporation and maintenance of histones at this locus, the cell employs an intricate network of molecular players, among which histone chaperones and chromatin remodelling factors have been identified over the past years. The mammalian centromere-specific chaperone HJURP represents an interesting paradigm to understand the functioning of this network. This review highlights and discusses the latest findings on centromeric histone H3 variant deposition and regulation to delineate the current view on centromere establishment, maintenance and propagation throughout the cell cycle. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.

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