Dynamique de la Chromatine

Publications de l’équipe

Année de publication : 2014

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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Année de publication : 2013

Carlos Rivera, Zachary A Gurard-Levin, Geneviève Almouzni, Alejandra Loyola (2013 Dec 17)

Histone lysine methylation and chromatin replication.

Biochimica et biophysica acta : 1433-9 : DOI : 10.1016/j.bbagrm.2014.03.009 En savoir plus
Résumé

In eukaryotic organisms, the replication of the DNA sequence and its organization into chromatin are critical to maintain genome integrity. Chromatin components, such as histone variants and histone post-translational modifications, along with the higher-order chromatin structure, impact several DNA metabolic processes, including replication, transcription, and repair. In this review we focus on lysine methylation and the relationships between this histone mark and chromatin replication. We first describe studies implicating lysine methylation in regulating early steps in the replication process. We then discuss chromatin reassembly following replication fork passage, where the incorporation of a combination of newly synthesized histones and parental histones can impact the inheritance of lysine methylation marks on the daughter strands. Finally, we elaborate on how the inheritance of lysine methylation can impact maintenance of the chromatin landscape, using heterochromatin as a model chromatin domain, and we discuss the potential mechanisms involved in this process.

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Roderick J O'Sullivan, Nausica Arnoult, Daniel H Lackner, Liana Oganesian, Candy Haggblom, Armelle Corpet, Genevieve Almouzni, Jan Karlseder (2013 Sep 20)

Rapid induction of alternative lengthening of telomeres by depletion of the histone chaperone ASF1.

Nature structural & molecular biology : 167-74 : DOI : 10.1038/nsmb.2754 En savoir plus
Résumé

The mechanism of activation of the alternative lengthening of telomeres (ALT) pathway of mammalian chromosome-end maintenance has been unclear. We have now discovered that co-depletion of the histone chaperones ASF1a and ASF1b in human cells induced all hallmarks of ALT in both primary and cancer cells. These included the formation of ALT-associated PML (promyelocytic leukemia) bodies (APBs), the presence of extrachromosomal telomeric DNA species, an elevated frequency of telomeric sister chromatid exchanges (t-SCE) events and intertelomeric exchange of an integrated tag. The induction of ALT characteristics in this setting led to the simultaneous suppression of telomerase. We determined that ALT induction is positively regulated by the proteins RAD17 and BLM and negatively regulated by EXO1 and DNA2. The induction of ALT phenotypes as a consequence of ASF1 depletion strongly supports the hypothesis that ALT is a consequence of histone management dysfunction.

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Rocío Montes de Oca, Zachary A Gurard-Levin, Frédérique Berger, Haniya Rehman, Elise Martel, Armelle Corpet, Leanne de Koning, Isabelle Vassias, Laurence O W Wilson, Didier Meseure, Fabien Reyal, Alexia Savignoni, Bernard Asselain, Xavier Sastre-Garau, Geneviève Almouzni (2013 Sep 11)

The histone chaperone HJURP is a new independent prognostic marker for luminal A breast carcinoma.

Molecular oncology : 657-74 : DOI : 10.1016/j.molonc.2014.11.002 En savoir plus
Résumé

Breast cancer is a heterogeneous disease with different molecular subtypes that have varying responses to therapy. An ongoing challenge in breast cancer research is to distinguish high-risk patients from good prognosis patients. This is particularly difficult in the low-grade, ER-positive luminal A tumors, where robust diagnostic tools to aid clinical treatment decisions are lacking. Recent data implicating chromatin regulators in cancer initiation and progression offers a promising avenue to develop new tools to help guide clinical decisions.

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Craig L Peterson, Genevieve Almouzni (2013 Sep 5)

Nucleosome dynamics as modular systems that integrate DNA damage and repair.

Cold Spring Harbor perspectives in biology : DOI : 10.1101/cshperspect.a012658 En savoir plus
Résumé

By some estimates, a eukaryotic cell must repair up to 10,000 DNA lesions per cell cycle to counteract endogenous sources of DNA damage. Exposure to environmental toxins, UV sources, or other radiations only increases this enormous number. Failure to repair such lesions can lead to a deleterious mutation rate, genomic instability, or cell death. The timely and efficient repair of eukaryotic DNA damage is further complicated by the realization that DNA lesions must be detected and repaired in the context of chromatin with its complex organization within the nucleus. Numerous studies have shown that chromatin packaging can inhibit nearly all repair pathways, and recent work has defined specific mechanisms that facilitate DNA repair within the chromatin context. In this review, we provide a broad overview of chromatin regulatory mechanisms, mainly at the nucleosomal level, and then focus on recent work that elucidates the role of chromatin structure in regulating the timely and efficient repair of DNA double-strand breaks (DSBs).

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Nicolas Lacoste, Adam Woolfe, Hiroaki Tachiwana, Ana Villar Garea, Teresa Barth, Sylvain Cantaloube, Hitoshi Kurumizaka, Axel Imhof, Geneviève Almouzni (2013 Jun 25)

Mislocalization of the centromeric histone variant CenH3/CENP-A in human cells depends on the chaperone DAXX.

Molecular cell : 631-44 : DOI : 10.1016/j.molcel.2014.01.018 En savoir plus
Résumé

Centromeres are essential for ensuring proper chromosome segregation in eukaryotes. Their definition relies on the presence of a centromere-specific H3 histone variant CenH3, known as CENP-A in mammals. Its overexpression in aggressive cancers raises questions concerning its effect on chromatin dynamics and contribution to tumorigenesis. We find that CenH3 overexpression in human cells leads to ectopic enrichment at sites of active histone turnover involving a heterotypic tetramer containing CenH3-H4 with H3.3-H4. Ectopic localization of this particle depends on the H3.3 chaperone DAXX rather than the dedicated CenH3 chaperone HJURP. This aberrant nucleosome occludes CTCF binding and has a minor effect on gene expression. Cells overexpressing CenH3 are more tolerant of DNA damage. Both the survival advantage and CTCF occlusion in these cells are dependent on DAXX. Our findings illustrate how changes in histone variant levels can disrupt chromatin dynamics and suggests a possible mechanism for cell resistance to anticancer treatments.

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David M MacAlpine, Geneviève Almouzni (2013 Jun 10)

Chromatin and DNA replication.

Cold Spring Harbor perspectives in biology : a010207 : DOI : 10.1101/cshperspect.a010207 En savoir plus
Résumé

The size of a eukaryotic genome presents a unique challenge to the cell: package and organize the DNA to fit within the confines of the nucleus while at the same time ensuring sufficient dynamics to allow access to specific sequences and features such as genes and regulatory elements. This is achieved via the dynamic nucleoprotein organization of eukaryotic DNA into chromatin. The basic unit of chromatin, the nucleosome, comprises a core particle with 147 bp of DNA wrapped 1.7 times around an octamer of histones. The nucleosome is a highly versatile and modular structure, both in its composition, with the existence of various histone variants, and through the addition of a series of posttranslational modifications on the histones. This versatility allows for both short-term regulatory responses to external signaling, as well as the long-term and multigenerational definition of large functional chromosomal domains within the nucleus, such as the centromere. Chromatin organization and its dynamics participate in essentially all DNA-templated processes, including transcription, replication, recombination, and repair. Here we will focus mainly on nucleosomal organization and describe the pathways and mechanisms that contribute to assembly of this organization and the role of chromatin in regulating the DNA replication program.

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Federico Abascal, Armelle Corpet, Zachary A Gurard-Levin, David Juan, Françoise Ochsenbein, Daniel Rico, Alfonso Valencia, Geneviève Almouzni (2013 May 2)

Subfunctionalization via adaptive evolution influenced by genomic context: the case of histone chaperones ASF1a and ASF1b.

Molecular biology and evolution : 1853-66 : DOI : 10.1093/molbev/mst086 En savoir plus
Résumé

Gene duplication is regarded as the main source of adaptive functional novelty in eukaryotes. Processes such as neo- and subfunctionalization impact the evolution of paralogous proteins where functional divergence is frequently key to retain the gene copies. Here, we examined antisilencing function 1 (ASF1), a conserved eukaryotic H3-H4 histone chaperone, involved in histone dynamics during replication, transcription, and DNA repair. Although yeast feature a single ASF1 protein, two paralogs exist in most vertebrates, termed ASF1a and ASF1b, with distinct cellular roles in mammals. To explain this division of tasks, we integrated evolutionary and comparative genomic analyses with biochemical and structural approaches. First, we show that a duplication event at the ancestor of jawed vertebrates, followed by ASF1a relocation into an intron of the minichromosome maintenance complex component 9 (MCM9) gene at the ancestor of tetrapods, provided a different genomic environment for each paralog with marked differences of GC content and DNA replication timing. Second, we found signatures of positive selection in the N- and C-terminal regions of ASF1a and ASF1b. Third, we demonstrate that regions outside the primary interaction surface are key for the preferential interactions of the human paralogs with distinct H3-H4 chaperones. On the basis of these data, we propose that ASF1 experienced subfunctionalization shaped by the adaptation of the genes to their respective genomic context, reflecting a case of genomic context-driven escape from adaptive conflict.

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Frederick Alt, Genevieve Almouzni (2013 May 1)

Genome architecture and expression.

Current opinion in genetics & development : 79-80 : DOI : 10.1016/j.gde.2013.04.005 En savoir plus
Résumé

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Salomé Adam, Sophie E Polo, Geneviève Almouzni (2013 Apr 26)

Transcription recovery after DNA damage requires chromatin priming by the H3.3 histone chaperone HIRA.

Cell : 94-106 : DOI : 10.1016/j.cell.2013.08.029 En savoir plus
Résumé

Understanding how to recover fully functional and transcriptionally active chromatin when its integrity has been challenged by genotoxic stress is a critical issue. Here, by investigating how chromatin dynamics regulate transcriptional activity in response to DNA damage in human cells, we identify a pathway involving the histone chaperone histone regulator A (HIRA) to promote transcription restart after UVC damage. Our mechanistic studies reveal that HIRA accumulates at sites of UVC irradiation upon detection of DNA damage prior to repair and deposits newly synthesized H3.3 histones. This local action of HIRA depends on ubiquitylation events associated with damage recognition. Furthermore, we demonstrate that the early and transient function of HIRA in response to DNA damage primes chromatin for later reactivation of transcription. We propose that HIRA-dependent histone deposition serves as a chromatin bookmarking system to facilitate transcription recovery after genotoxic stress.

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Dan Filipescu, Emmanuelle Szenker, Geneviève Almouzni (2013 Apr 12)

Developmental roles of histone H3 variants and their chaperones.

Trends in genetics : TIG : 630-40 : DOI : 10.1016/j.tig.2013.06.002 En savoir plus
Résumé

Animal development and lifetime potential exploit a balance between the stability and plasticity of cellular identity. Within the nucleus, this is controlled by an interplay involving lineage-specific transcription factors and chromatin dynamics. Histone H3 variants contribute to chromatin dynamics through the timing and sites of their incorporation, promoted by dedicated histone chaperones. Moreover, their individual modifications and binding partners provide distinct features at defined genomic loci. We highlight here the importance of the H3.3 replacement variant for the nuclear reprogramming that occurs during gametogenesis, fertilization, and germline establishment. Furthermore, we describe how the recently characterized H3.3 dynamics associated with gastrulation, myogenesis, or neurogenesis underline the role of chromatin changes in cell differentiation. Finally, we discuss the challenges of maintaining centromeric identity through propagation of the centromeric CenH3 variant in different cell types. Future challenges will be to gain a comprehensive picture of H3 variants and their chaperones during development and differentiation.

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