Mammalian Developmental Epigenetics

Keywords: epigenetic, X inactivation, mouse development, chromatin, nuclear organization

Read the scientific activity report. (pdf 1.7Mo, last update 9th, february 2010)

In female mammals, one of the two X chromosomes is transcriptionally silenced during early development to compensate for the double ‘dose' of X-linked gene products in females (XX) when compared to males (XY). This process, known as X inactivation, represents a paradigm for developmental epigenetics.

One of the most striking aspects of X inactivation is that the entire chromosome is silenced whereas its homologue, present in the same nucleus, remains active. A unique locus, the X-inactivation centre (Xic), initiates this process. The Xic produces a non-coding, regulatory RNA called Xist, which “coats” the X chromosome to be inactivated. We are interested in understanding the basis of monoallelic regulation during X inactivation, the function of the Xist transcript and the epigenetic mechanisms that provide the cellular memory of the inactive state, including chromatin proteins, non-coding RNAs and DNA methylation. Understanding the epigenetics of X inactivation should provide important insights into diseases such as cancer, where epigenetic deregulation plays an important role.

To define the developmental regulation, as well as the genetic and epigenetic requirements of X inactivation in different embryonic lineages, our group uses a combination of molecular genetics and cell biology approaches to study mouse embryos and embryonic stem cells. We are particularly interested in the roles that chromatin factors, non-coding RNAs and nuclear organisation might play in X inactivation. To this end we use multi-dimensional fluorescence imaging techniques, in both fixed and living cells, as well as epigenomic approaches.

Our studies on mouse embryos have shown that X inactivation is a highly dynamic process during early embryogenesis (Fig. 1).

Fig. 1 

In mice, the paternal X chromosome (Xp) undergoes an imprinted form of X inactivation. Our studies (Okamoto et al, 2004) have shown that this imprinted form of X inactivation occurs much earlier than previously thought (at the 4-8 cell stage) and is due to imprinting at the Xic locus (imprinted Xist expression). We also showed that in the inner cell mass (ICM) of the blastocyst, the Xp becomes reactivated. This occurs just prior to the random inactivation of either the paternal or maternal X chromosome that occurs in cells that give rise to the embryo proper. Paternal X reactivation reveals the plasticity of the inactive state during early development and underlines the importance of the ICM in the global reprogramming of epigenetic marks in the embryo.

The basis for the monoallelic regulation of random X inactivation remains a major question in the field. We recently showed that the locus that controls the initiation of X inactivation (the Xic) is involved in dynamic trans-interactions (Fig. 2).

Fig. 2 

We believe that these interactions participate in a process that enables a cell to sense the number of X chromosomes and thus trigger X inactivation, if more than two X chromosomes are present Xic pairing may also enable the monoallelic regulation of the Xist gene. Xic pairing (Fig. 3) represents one of the first examples of developmentally regulated trans-interactions between homologous loci in mammalian cells.

Fig. 3 

The role of Xist RNA in silencing the X chromosome also remains a mystery. We recently gained insight into one of Xist RNA's roles in X inactivation, by showing that it creates a silent nuclear compartment into which genes become recruited when they are silenced (Fig. 4).

Fig. 4 

This recruitment likely participates in maintaining the inactive state and reinforces the idea that nuclear compartmentalization plays an important role in epigenetic processes.

Our laboratory mission is to define the mechanisms underlying X inactivation during development and to use X inactivation as a model system with which to explore epigenetics in cancer.

In this context, our current aims are:

• to investigate the sequence and epigenetic requirements of X inactivation
• to explore the epigenetic plasticity of the inactive state during development and in somatic versus tumour cells
• to define nuclear dynamics of the Xic and the role of nuclear compartmentalization in X inactivation
• to explore the role of Xist RNA and other non-coding RNAs in X inactivation

Last update: February 2010

Key publications

2007

• Augui S., Filion G., Huart S., Guggiari M., Maresca M., Stewart F. & Heard E.
  Sensing X-chromosome pairs prior to X inactivation via a novel X-pairing region of the Xic
  Science, 318, 1632-1636
• Vincent-Salomon A., Ganem-Elbaz C., Manie E., Raynal V., Sastre-Garau X., Stoppa-Lyonnet D., Stern M.H. & Heard E.
  X-inactive-specific transcript RNA coating and genetic instability of the X chromosome in BRCA1 breast tumors
  Cancer Research, 67, 5134-5140

2006

• Chaumeil J., Le Baccon P.,Wutz A. & Heard E.
  A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced
  Genes & Dev., 20, 2223-2237

2005

• Okamoto I., Arnaud D., Le Baccon P., Otte A.P., Disteche C., Avner P. et Heard E.
  Imprinted inactivation of the paternal X chromosome in mice occurs de novo
  Nature, 438(7066):369-73

2004

• Okamoto I., Otte A., Allis C. D., Reinberg D. et Heard E.
  "Epigenetic dynamics of imprinted X inactivation during early mouse development"
  Science, 303, 644-649