Home › Research groups › Mammalian developmental epigenetics

Mammalian developmental epigenetics

Imprimer la page

-A +A
Group Leader : Professor Edith Heard
Heard_Team

Keywords

Epigenetics, X-chromosome inactivation, Chromatin, Mouse development, Nuclear organization

Plain english

In female mammals, one of the two X chromosomes is transcriptionally silenced during early development, a process that allows for dosage compensation between XX females and XY males. This process, known as X-chromosome inactivation, is a paradigm for developmental epigenetics.

 

 

 

 

 

 

 

Our goal

Understanding the regulation of gene expression during normal development is crucial for our comprehension of the alterations that can lead to cancer. Using the process of X-chromosome inactivation as a model system, we are developing approaches that allow us to gain insights into the fundamental mechanisms that underlie the dynamics of gene expression during development and cellular differentiation, as well as during tumorigenesis.

Females are mosaicsFemales are mosaics

Why study X-chromosome inactivation?

During development, specialized cell types emerge from a common single progenitor thanks to the expression of specific sets of genes, and the silencing of other genes. The differences between cell types are not due to DNA sequence differences but rather to what is often referred to as epigenetic variation.

The aim of the group of Edith Heard is to understand how cells can express their genomes differentially and in a stable, although sometimes reversible, manner during development, using X-chromosome inactivation as our model. X inactivation is a normal process, entailing the silencing of one of the two X chromosomes in female mammals. Once established the silent state is stably maintained through cell divisions and throughout the adult life, but can be reversed at certain stages of development, in the germ line and possibly in cancer cells. The inactive X provides a unique model of chromosome-wide epigenetic silencing.

The X-chromosome inactivation cycle in the mouseThe X-chromosome inactivation cycle in the mouse

Our questions

Studying the process of X chromosome inactivation allows to unveil molecular mechanisms involved in establishing, maintaining and reversing heterochromatin. We are interested in four principal questions :

  • What underlies the control of the initiation of X-chromosome inactivation?
  • How is transcriptional repression established?
  • How is the inactive state faithfully inherited through cellular division?  
  • How does tumor development affect maintenance of the inactive state of the X chromosome ?
Nucleus organisation at the onset of X-chromosome inactivationNucleus organisation at the onset of X-chromosome inactivation

Our tools

To analyse the early steps of X-chromosome inactivation we study mouse embryos and mouse embryonic stem cells. In parallel, we also use human cancer cell lines, as well as breast tumor samples in collaboration with doctors at the Curie Hospital, to investigate the mechanisms underlying epigenetic instability in the context of tumor development.

We couple classic molecular approaches with the analysis of cellular behavior at the single-cell level, in fixed or live samples, thanks to the the Institut Curie’s imaging platform and the state-of-the-art microscopy tools and expertise available within the Genetics and Developmental Biology department. These approaches are combined with large-scale genomic and epigenomic techniques made possible thanks to the various technological departments of the Institut Curie. Our work is especially focused on changes in chromatin structure and nuclear organization associated with heterochromatin formation, as well as the role of non-coding RNAs such as the remarkable Xist RNA which is expressed specifically from the inactive X and underlies the initiation of X inactivation.

Xist RNA coating of the inactive X chromosomeXist RNA coating of the inactive X chromosome

Key publications

  • Year of publication : 2013

  • Catherine Corbel, Patricia Diabangouaya, Anne-Valerie Gendrel, Jennifer Chow, Edith Heard (2013 Feb) Unusual chromatin status and organization of the inactive X chromosome in murine trophoblast giant cells.

    Development (Cambridge, England), 140(4): 861-72
    Mammalian X-chromosome inactivation (XCI) enables dosage compensation between XX females and XY males. It is an essential process and its absence in XX individuals results in early lethality due primarily to extra-embryonic defects. This sensitivity to X-linked gene dosage in extra-embryonic tissues is difficult to reconcile with the reported tendency of escape from XCI in these tissues. The precise transcriptional status of the inactive X chromosome in different lineages has mainly been examined using transgenes or in in vitro differentiated stem cells and the degree to which endogenous X-linked genes are silenced in embryonic and extra-embryonic lineages during early postimplantation stages is unclear. Here we investigate the precise temporal and lineage-specific X-inactivation status of several genes in postimplantation mouse embryos. We find stable gene silencing in most lineages, with significant levels of escape from XCI mainly in one extra-embryonic cell type: trophoblast giant cells (TGCs). To investigate the basis of this epigenetic instability, we examined the chromatin structure and organization of the inactive X chromosome in TGCs obtained from ectoplacental cone explants. We find that the Xist RNA-coated X chromosome has a highly unusual chromatin content in TGCs, presenting both heterochromatic marks such as H3K27me3 and euchromatic marks such as histone H4 acetylation and H3K4 methylation. Strikingly, Xist RNA does not form an overt silent nuclear compartment or Cot1 hole in these cells. This unusual combination of silent and active features is likely to reflect, and might underlie, the partial activity of the X chromosome in TGCs.
    Read more

  • Year of publication : 2012

  • Elphège Nora, Bryan Lajoie, Edda Schulz, Luca Giorgetti, Ikuhiro Okamoto, Nicolas Servant, Tristan Piolot, Nynke Berkum, Johannes Meisig, John Sedat, Joost Gribnau, Emmanuel Barillot, Nils Blüthgen, Job Dekker, Edith Heard (2012 May 17) Spatial partitioning of the regulatory landscape of the X-inactivation centre.

    Nature, 485(7398): 381-5
    In eukaryotes transcriptional regulation often involves multiple long-range elements and is influenced by the genomic environment. A prime example of this concerns the mouse X-inactivation centre (Xic), which orchestrates the initiation of X-chromosome inactivation (XCI) by controlling the expression of the non-protein-coding Xist transcript. The extent of Xic sequences required for the proper regulation of Xist remains unknown. Here we use chromosome conformation capture carbon-copy (5C) and super-resolution microscopy to analyse the spatial organization of a 4.5-megabases (Mb) region including Xist. We discover a series of discrete 200-kilobase to 1 Mb topologically associating domains (TADs), present both before and after cell differentiation and on the active and inactive X. TADs align with, but do not rely on, several domain-wide features of the epigenome, such as H3K27me3 or H3K9me2 blocks and lamina-associated domains. TADs also align with coordinately regulated gene clusters. Disruption of a TAD boundary causes ectopic chromosomal contacts and long-range transcriptional misregulation. The Xist/Tsix sense/antisense unit illustrates how TADs enable the spatial segregation of oppositely regulated chromosomal neighbourhoods, with the respective promoters of Xist and Tsix lying in adjacent TADs, each containing their known positive regulators. We identify a novel distal regulatory region of Tsix within its TAD, which produces a long intervening RNA, Linx. In addition to uncovering a new principle of cis-regulatory architecture of mammalian chromosomes, our study sets the stage for the full genetic dissection of the X-inactivation centre.
    Read more

  • Year of publication : 2011

  • Osamu Masui, Isabelle Bonnet, Patricia Le Baccon, Isabel Brito, Tim Pollex, Niall Murphy, Philippe Hupé, Emmanuel Barillot, Andrew Belmont, Edith Heard (2011 Apr 29) Live-cell chromosome dynamics and outcome of X chromosome pairing events during ES cell differentiation.

    Cell, 145(3): 447-58
    Random X inactivation represents a paradigm for monoallelic gene regulation during early ES cell differentiation. In mice, the choice of X chromosome to inactivate in XX cells is ensured by monoallelic regulation of Xist RNA via its antisense transcription unit Tsix/Xite. Homologous pairing events have been proposed to underlie asymmetric Tsix expression, but direct evidence has been lacking owing to their dynamic and transient nature. Here we investigate the live-cell dynamics and outcome of Tsix pairing in differentiating mouse ES cells. We find an overall increase in genome dynamics including the Xics during early differentiation. During pairing, however, Xic loci show markedly reduced movements. Upon separation, Tsix expression becomes transiently monoallelic, providing a window of opportunity for monoallelic Xist upregulation. Our findings reveal the spatiotemporal choreography of the X chromosomes during early differentiation and indicate a direct role for pairing in facilitating symmetry-breaking and monoallelic regulation of Xist during random X inactivation.
    Read more

  • Ikuhiro Okamoto, Catherine Patrat, Dominique Thépot, Nathalie Peynot, Patricia Fauque, Nathalie Daniel, Patricia Diabangouaya, Jean-Philippe Wolf, Jean-Paul Renard, Véronique Duranthon, Edith Heard (2011 Apr 21) Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development.

    Nature, 472(7343): 370-4
    X-chromosome inactivation (XCI) in female mammals allows dosage compensation for X-linked gene products between the sexes. The developmental regulation of this process has been extensively investigated in mice, where the X chromosome of paternal origin (Xp) is silenced during early embryogenesis owing to imprinted expression of the regulatory RNA, Xist (X-inactive specific transcript). Paternal XCI is reversed in the inner cell mass of the blastocyst and random XCI subsequently occurs in epiblast cells. Here we show that other eutherian mammals have very different strategies for initiating XCI. In rabbits and humans, the Xist homologue is not subject to imprinting and XCI begins later than in mice. Furthermore, Xist is upregulated on both X chromosomes in a high proportion of rabbit and human embryo cells, even in the inner cell mass. In rabbits, this triggers XCI on both X chromosomes in some cells. In humans, chromosome-wide XCI has not initiated even by the blastocyst stage, despite the upregulation of XIST. The choice of which X chromosome will finally become inactive thus occurs downstream of Xist upregulation in both rabbits and humans, unlike in mice. Our study demonstrates the remarkable diversity in XCI regulation and highlights differences between mammals in their requirement for dosage compensation during early embryogenesis.
    Read more