Dynamique de la Chromatine

Publications de l’équipe

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
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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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Miguel Casanova, Michał Pasternak, Fatima El Marjou, Patricia Le Baccon, Aline V Probst, Geneviève Almouzni (2013 Jan 3)

Heterochromatin reorganization during early mouse development requires a single-stranded noncoding transcript.

Cell reports : 1156-67 : DOI : 10.1016/j.celrep.2013.08.015 En savoir plus
Résumé

The equalization of pericentric heterochromatin from distinct parental origins following fertilization is essential for genome function and development. The recent implication of noncoding transcripts in this process raises questions regarding the connection between RNA and the nuclear organization of distinct chromatin environments. Our study addresses the interrelationship between replication and transcription of the two parental pericentric heterochromatin (PHC) domains and their reorganization during early embryonic development. We demonstrate that the replication of PHC is dispensable for its clustering at the late two-cell stage. In contrast, using parthenogenetic embryos, we show that pericentric transcripts are essential for this reorganization independent of the chromatin marks associated with the PHC domains. Finally, our discovery that only reverse pericentric transcripts are required for both the nuclear reorganization of PHC and development beyond the two-cell stage challenges current views on heterochromatin organization.

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Année de publication : 2012

Elina Zueva, Rhys S Allan, Florence Cammas, Heidi A Schreiber, Vanessa Masson, Gabrielle T Belz, Danièle Roche, Christèle Maison, Jean-Pierre Quivy, Geneviève Almouzni, Sebastian Amigorena (2012 Dec 21)

[Epigenetic control of Th2 helper cell differentiation by the Suv39h1/HP1α pathway].

Médecine sciences : M/S : 1032-4 : DOI : 10.1051/medsci/20122812003 En savoir plus
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Salomé Adam, Sophie E Polo (2012 Aug 21)

Chromatin dynamics during nucleotide excision repair: histones on the move.

International journal of molecular sciences : 11895-911 : DOI : 10.3390/ijms130911895 En savoir plus
Résumé

It has been a long-standing question how DNA damage repair proceeds in a nuclear environment where DNA is packaged into chromatin. Several decades of analysis combining in vitro and in vivo studies in various model organisms ranging from yeast to human have markedly increased our understanding of the mechanisms underlying chromatin disorganization upon damage detection and re-assembly after repair. Here, we review the methods that have been developed over the years to delineate chromatin alterations in response to DNA damage by focusing on the well-characterized Nucleotide Excision Repair (NER) pathway. We also highlight how these methods have provided key mechanistic insight into histone dynamics coupled to repair in mammals, raising new issues about the maintenance of chromatin integrity. In particular, we discuss how NER factors and central players in chromatin dynamics such as histone modifiers, nucleosome remodeling factors, and histone chaperones function to mobilize histones during repair.

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Jerome Jullien, Carolina Astrand, Emmanuelle Szenker, Nigel Garrett, Genevieve Almouzni, John B Gurdon (2012 Jul 27)

HIRA dependent H3.3 deposition is required for transcriptional reprogramming following nuclear transfer to Xenopus oocytes.

Epigenetics & chromatin : 17 : DOI : 10.1186/1756-8935-5-17 En savoir plus
Résumé

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Sylvain Cantaloube, Kelly Romeo, Patricia Le Baccon, Geneviève Almouzni, Jean-Pierre Quivy (2012 Mar 27)

Characterization of chromatin domains by 3D fluorescence microscopy: An automated methodology for quantitative analysis and nuclei screening.

BioEssays : news and reviews in molecular, cellular and developmental biology : 509-17 : DOI : 10.1002/bies.201100188 En savoir plus
Résumé

Fluorescence microscopy has provided a route to qualitatively analyze features of nuclear structures and chromatin domains with increasing resolution. However, it is becoming increasingly important to develop tools for quantitative analysis. Here, we present an automated method to quantitatively determine the enrichment of several endogenous factors, immunostained in pericentric heterochromatin domains in mouse cells. We show that this method permits an unbiased characterization of changes in the enrichment of several factors with statistical significance from a large number of nuclei. Furthermore, the nuclei can be sorted according to the enrichment value of these factors. This method should prove useful to monitor events related to changes in the amount, rather than the presence or absence, of any factor. By adapting a few parameters, it could be extended to other nuclear structures and the benefit of using available software will permit its use in many biological labs.

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