Épigenèse et développement des mammifères

Publications de l’équipe

Année de publication : 2015

Jean-Louis Guénet, Jean-Jacques Panthier, Philip Avner, Edith Heard, Xavier Montagutelli (2015 Jul 9)

[The legacy of Mary F. Lyon (1925-2014)].

Médecine sciences : M/S : 687-9 : DOI : 10.1051/medsci/20153106024 En savoir plus
Résumé

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Rafael Galupa, Edith Heard (2015 May 26)

X-chromosome inactivation: new insights into cis and trans regulation.

Current opinion in genetics & development : 57-66 : DOI : 10.1016/j.gde.2015.04.002 En savoir plus
Résumé

X-chromosome inactivation (XCI) is a developmentally associated process that evolved in mammals to enable gene dosage compensation between XX and XY individuals. In placental mammals, it is triggered by the long noncoding RNA Xist, which is produced from a complex regulatory locus, the X-inactivation centre (Xic). Recent insights into the regulatory landscape of the Xic, including its partitioning into topological associating domains (TADs) and its genetic dissection, have important implications for the monoallelic regulation of Xist. Here, we present some of the latest studies on X inactivation with a special focus on the regulation of Xist, its various functions and the putative role of chromosome conformation in regulating the dynamics of this locus during development and differentiation.

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Ronan Chaligné, Tatiana Popova, Marco-Antonio Mendoza-Parra, Mohamed-Ashick M Saleem, David Gentien, Kristen Ban, Tristan Piolot, Olivier Leroy, Odette Mariani, Hinrich Gronemeyer, Anne Vincent-Salomon, Marc-Henri Stern, Edith Heard (2015 Feb 6)

The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer.

Genome research : 488-503 : DOI : 10.1101/gr.185926.114 En savoir plus
Résumé

Disappearance of the Barr body is considered a hallmark of cancer, although whether this corresponds to genetic loss or to epigenetic instability and transcriptional reactivation is unclear. Here we show that breast tumors and cell lines frequently display major epigenetic instability of the inactive X chromosome, with highly abnormal 3D nuclear organization and global perturbations of heterochromatin, including gain of euchromatic marks and aberrant distributions of repressive marks such as H3K27me3 and promoter DNA methylation. Genome-wide profiling of chromatin and transcription reveal modified epigenomic landscapes in cancer cells and a significant degree of aberrant gene activity from the inactive X chromosome, including several genes involved in cancer promotion. We demonstrate that many of these genes are aberrantly reactivated in primary breast tumors, and we further demonstrate that epigenetic instability of the inactive X can lead to perturbed dosage of X-linked factors. Taken together, our study provides the first integrated analysis of the inactive X chromosome in the context of breast cancer and establishes that epigenetic erosion of the inactive X can lead to the disappearance of the Barr body in breast cancer cells. This work offers new insights and opens up the possibility of exploiting the inactive X chromosome as an epigenetic biomarker at the molecular and cytological levels in cancer.

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Luca Giorgetti, Tristan Piolot, Edith Heard (2015 Jan 4)

High-resolution 3D DNA FISH using plasmid probes and computational correction of optical aberrations to study chromatin structure at the sub-megabase scale.

Methods in molecular biology (Clifton, N.J.) : 37-53 : DOI : 10.1007/978-1-4939-2253-6_3 En savoir plus
Résumé

Characterizing the three-dimensional organization of chromosomes is a fundamental goal in molecular biology and will be critical to understand how gene expression is regulated by distal regulatory sequences such as enhancers. Chromosome conformation capture (3C) techniques have recently revealed that the interactions between regulatory elements appear to occur in the context of topologically associating domains (TADs), each spanning few hundreds kilobases, within which the chromatin fiber preferentially interacts. However, 3C-based data represent average interaction probabilities of the chromatin fiber over millions of cells. To understand how variable chromatin conformation is within each TAD, one needs to employ single-cell techniques such as 3D DNA FISH. Given the small size of TADs however (typically <1 Mb), classical DNA FISH design needs to be adapted to achieve high genomic and spatial resolution. Here, we describe a high-resolution 3D DNA FISH approach we recently developed, based on a combination of short plasmid probes and computational correction of optical aberrations. We describe probe design and generation and the 3D DNA FISH procedure. We further discuss how to optimize microscope settings and to implement calibration-bead-assisted computational corrections in order to achieve 50 nm resolution in two-color distance measurements between probes that can be as close as 50 kb along the genome.

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Année de publication : 2014

Catherine Patrat, Ikuhiro Okamoto, Edith Heard (2014 Aug 29)

[Initiation of X chromosome inactivation during early embryogenesis in mice and in humans].

Bulletin de l'Académie nationale de médecine : 609-17 En savoir plus
Résumé

X chromosome inactivation (XCI) is a very good model of epigenetic changes that occur during early development. This essential process occurring in females leads to X-linked gene dosage compensation between the sexes. Recent data suggest that different mammalian species may use different strategies to initiate XCI during early embryogenesis. In mice, XCI occurs in two waves, imprinted during preimplantation then random in the embryo. In humans, XCI is not imprinted and has not yet been triggered at the blastocyst stage. These results highlight the remarkable diversity of XCI mechanisms.

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Anne-Valerie Gendrel, Edith Heard (2014 Jul 9)

Noncoding RNAs and epigenetic mechanisms during X-chromosome inactivation.

Annual review of cell and developmental biology : 561-80 : DOI : 10.1146/annurev-cellbio-101512-122415 En savoir plus
Résumé

In mammals, the process of X-chromosome inactivation ensures equivalent levels of X-linked gene expression between males and females through the silencing of one of the two X chromosomes in female cells. The process is established early in development and is initiated by a unique locus, which produces a long noncoding RNA, Xist. The Xist transcript triggers gene silencing in cis by coating the future inactive X chromosome. It also induces a cascade of chromatin changes, including posttranslational histone modifications and DNA methylation, and leads to the stable repression of all X-linked genes throughout development and adult life. We review here recent progress in our understanding of the molecular mechanisms involved in the initiation of Xist expression, the propagation of the Xist RNA along the chromosome, and the cis-elements and trans-acting factors involved in the maintenance of the repressed state. We also describe the diverse strategies used by nonplacental mammals for X-chromosome dosage compensation and highlight the common features and differences between eutherians and metatherians, in particular regarding the involvement of long noncoding RNAs.

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Ronan Chaligné, Edith Heard (2014 Jun 18)

X-chromosome inactivation in development and cancer.

FEBS letters : 2514-22 : DOI : 10.1016/j.febslet.2014.06.023 En savoir plus
Résumé

X-chromosome inactivation represents an epigenetics paradigm and a powerful model system of facultative heterochromatin formation triggered by a non-coding RNA, Xist, during development. Once established, the inactive state of the Xi is highly stable in somatic cells, thanks to a combination of chromatin associated proteins, DNA methylation and nuclear organization. However, sporadic reactivation of X-linked genes has been reported during ageing and in transformed cells and disappearance of the Barr body is frequently observed in cancer cells. In this review we summarise current knowledge on the epigenetic changes that accompany X inactivation and discuss the extent to which the inactive X chromosome may be epigenetically or genetically perturbed in breast cancer.

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Luca Giorgetti, Rafael Galupa, Elphège P Nora, Tristan Piolot, France Lam, Job Dekker, Guido Tiana, Edith Heard (2014 May 1)

Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription.

Cell : 950-63 : DOI : 10.1016/j.cell.2014.03.025 En savoir plus
Résumé

A new level of chromosome organization, topologically associating domains (TADs), was recently uncovered by chromosome conformation capture (3C) techniques. To explore TAD structure and function, we developed a polymer model that can extract the full repertoire of chromatin conformations within TADs from population-based 3C data. This model predicts actual physical distances and to what extent chromosomal contacts vary between cells. It also identifies interactions within single TADs that stabilize boundaries between TADs and allows us to identify and genetically validate key structural elements within TADs. Combining the model’s predictions with high-resolution DNA FISH and quantitative RNA FISH for TADs within the X-inactivation center (Xic), we dissect the relationship between transcription and spatial proximity to cis-regulatory elements. We demonstrate that contacts between potential regulatory elements occur in the context of fluctuating structures rather than stable loops and propose that such fluctuations may contribute to asymmetric expression in the Xic during X inactivation.

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Edith Heard, Robert A Martienssen (2014 Apr 1)

Transgenerational epigenetic inheritance: myths and mechanisms.

Cell : 95-109 : DOI : 10.1016/j.cell.2014.02.045 En savoir plus
Résumé

Since the human genome was sequenced, the term « epigenetics » is increasingly being associated with the hope that we are more than just the sum of our genes. Might what we eat, the air we breathe, or even the emotions we feel influence not only our genes but those of descendants? The environment can certainly influence gene expression and can lead to disease, but transgenerational consequences are another matter. Although the inheritance of epigenetic characters can certainly occur-particularly in plants-how much is due to the environment and the extent to which it happens in humans remain unclear.

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Anne-Valerie Gendrel, Mikael Attia, Chong-Jian Chen, Patricia Diabangouaya, Nicolas Servant, Emmanuel Barillot, Edith Heard (2014 Feb 24)

Developmental dynamics and disease potential of random monoallelic gene expression.

Developmental cell : 366-80 : DOI : 10.1016/j.devcel.2014.01.016 En savoir plus
Résumé

X chromosome inactivation (XCI) and allelic exclusion of olfactory receptors or immunoglobulin loci represent classic examples of random monoallelic expression (RME). RME of some single copy genes has also been reported, but the in vivo relevance of this remains unclear. Here we identify several hundred RME genes in clonal neural progenitor cell lines derived from embryonic stem cells. RME occurs during differentiation, and, once established, the monoallelic state can be highly stable. We show that monoallelic expression also occurs in vivo, in the absence of DNA sequence polymorphism. Several of the RME genes identified play important roles in development and have been implicated in human autosomal-dominant disorders. We propose that monoallelic expression of such genes contributes to the fine-tuning of the developmental regulatory pathways they control, and, in the context of a mutation, RME can predispose to loss of function in a proportion of cells and thus contribute to disease.

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Edda G Schulz, Johannes Meisig, Tomonori Nakamura, Ikuhiro Okamoto, Anja Sieber, Christel Picard, Maud Borensztein, Mitinori Saitou, Nils Blüthgen, Edith Heard (2014 Feb 6)

The two active X chromosomes in female ESCs block exit from the pluripotent state by modulating the ESC signaling network.

Cell stem cell : 203-16 : DOI : 10.1016/j.stem.2013.11.022 En savoir plus
Résumé

During early development of female mouse embryos, both X chromosomes are transiently active. X gene dosage is then equalized between the sexes through the process of X chromosome inactivation (XCI). Whether the double dose of X-linked genes in females compared with males leads to sex-specific developmental differences has remained unclear. Using embryonic stem cells with distinct sex chromosome compositions as a model system, we show that two X chromosomes stabilize the naive pluripotent state by inhibiting MAPK and Gsk3 signaling and stimulating the Akt pathway. Since MAPK signaling is required to exit the pluripotent state, differentiation is paused in female cells as long as both X chromosomes are active. By preventing XCI or triggering it precociously, we demonstrate that this differentiation block is released once XX cells have undergone X inactivation. We propose that double X dosage interferes with differentiation, thus ensuring a tight coupling between X chromosome dosage compensation and development.

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Simão Teixeira da Rocha, Valentina Boeva, Martin Escamilla-Del-Arenal, Katia Ancelin, Camille Granier, Neuza Reis Matias, Serena Sanulli, Jen Chow, Edda Schulz, Christel Picard, Syuzo Kaneko, Kristian Helin, Danny Reinberg, A Francis Stewart, Anton Wutz, Raphaël Margueron, Edith Heard (2014 Jan 23)

Jarid2 Is Implicated in the Initial Xist-Induced Targeting of PRC2 to the Inactive X Chromosome.

Molecular cell : 301-16 : DOI : 10.1016/j.molcel.2014.01.002 En savoir plus
Résumé

During X chromosome inactivation (XCI), the Polycomb Repressive Complex 2 (PRC2) is thought to participate in the early maintenance of the inactive state. Although Xist RNA is essential for the recruitment of PRC2 to the X chromosome, the precise mechanism remains unclear. Here, we demonstrate that the PRC2 cofactor Jarid2 is an important mediator of Xist-induced PRC2 targeting. The region containing the conserved B and F repeats of Xist is critical for Jarid2 recruitment via its unique N-terminal domain. Xist-induced Jarid2 recruitment occurs chromosome-wide independently of a functional PRC2 complex, unlike at other parts of the genome, such as CG-rich regions, where Jarid2 and PRC2 binding are interdependent. Conversely, we show that Jarid2 loss prevents efficient PRC2 and H3K27me3 enrichment to Xist-coated chromatin. Jarid2 thus represents an important intermediate between PRC2 and Xist RNA for the initial targeting of the PRC2 complex to the X chromosome during onset of XCI.

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Année de publication : 2013

Luca Giorgetti, Nicolas Servant, Edith Heard (2013 Dec 26)

Changes in the organization of the genome during the mammalian cell cycle.

Genome biology : 142 : DOI : 10.1186/gb4147 En savoir plus
Résumé

By using chromosome conformation capture technology, a recent study has revealed two alternative three-dimensional folding states of the human genome during the cell cycle.

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Tim Pollex, Tristan Piolot, Edith Heard (2013 Aug 28)

Live-cell imaging combined with immunofluorescence, RNA, or DNA FISH to study the nuclear dynamics and expression of the X-inactivation center.

Methods in molecular biology (Clifton, N.J.) : 13-31 : DOI : 10.1007/978-1-62703-526-2_2 En savoir plus
Résumé

Differentiation of embryonic stem cells is accompanied by changes of gene expression and chromatin and chromosome dynamics. One of the most impressive examples for these changes is inactivation of one of the two X chromosomes occurring upon differentiation of mouse female embryonic stem cells. With a few exceptions, these events have been mainly studied in fixed cells. In order to better understand the dynamics, kinetics, and order of events during differentiation, one needs to employ live-cell imaging techniques. Here, we describe a combination of live-cell imaging with techniques that can be used in fixed cells (e.g., RNA FISH) to correlate locus dynamics or subnuclear localization with, e.g., gene expression. To study locus dynamics in female ES cells, we generated cell lines containing TetO arrays in the X-inactivation center, the locus on the X chromosome regulating X-inactivation, which can be visualized upon expression of TetR fused to fluorescent proteins. We will use this system to elaborate on how to generate ES cell lines for live-cell imaging of locus dynamics, how to culture ES cells prior to live-cell imaging, and to describe typical live-cell imaging conditions for ES cells using different microscopes. Furthermore, we will explain how RNA, DNA FISH, or immunofluorescence can be applied following live-cell imaging to correlate gene expression with locus dynamics.

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Elphège P Nora, Job Dekker, Edith Heard (2013 Jul 9)

Segmental folding of chromosomes: a basis for structural and regulatory chromosomal neighborhoods?

BioEssays : news and reviews in molecular, cellular and developmental biology : 818-28 : DOI : 10.1002/bies.201300040 En savoir plus
Résumé

We discuss here a series of testable hypotheses concerning the role of chromosome folding into topologically associating domains (TADs). Several lines of evidence suggest that segmental packaging of chromosomal neighborhoods may underlie features of chromatin that span large domains, such as heterochromatin blocks, association with the nuclear lamina and replication timing. By defining which DNA elements preferentially contact each other, the segmentation of chromosomes into TADs may also underlie many properties of long-range transcriptional regulation. Several observations suggest that TADs can indeed provide a structural basis to regulatory landscapes, by controlling enhancer sharing and allocation. We also discuss how TADs may shape the evolution of chromosomes, by causing maintenance of synteny over large chromosomal segments. Finally we suggest a series of experiments to challenge these ideas and provide concrete examples illustrating how they could be practically applied.

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