Sex chromosomes, development and diseases

In the Rougeulle lab, we study the emblematic process of X chromosome inactivation. We aim at elucidating how such a chromosome-wide epigenetic silencing is achieved and regulated during early human development. We have previously interrogated how lncRNAs, including XIST and its non-coding regulators, participate in the regulation of X chromosome activity. We now explore how X-inactivation may impact human development, fertility and how it may contribute to sex dimorphisms and to differences in disease incidence and manifestations in females compared to males. We also use non-human primate species to understand the evolution of X inactivation at a short evolutionary timescale.

The X chromosome is one of the largest chromosomes in humans, carrying up to 1100 genes with essential functions notably in the immune and nervous systems. In XX females, one of the X-chromosomes is subject to a unique epigenetic process leading to the global silencing of the majority of X-linked genes. This X chromosome inactivation (XCI) results in dosage compensation of X-linked gene expression with XY males and has fundamental consequences for human health and, potentially, fertility. Indeed, XCI takes place around the time of implantation and may therefore impact the development of female embryos. Moreover, skewed XCI towards one or the other X may severely affect the phenotypic manifestation of X-linked mutations in heterozygous females during development and in adulthood. In addition, several X-linked genes are known to escape from XCI, either constitutively or in a context-dependent manner, resulting in dosage imbalance and very few studies have actually addressed how fixed or unchanging the X chromosome inactive state is in fully differentiated solid tissues. This may contribute to sexual dimorphisms and sex-specific susceptibility to various pathologies, including cancers.

The main projects we are developing in the lab aim at connecting XCI and physiology by asking:

• When and where dosage compensation of X chromosome expression is required?
• Which X-linked genes are dosage sensitive (at the transcription, RNA and protein levels)?
• What are the differences in XCI between lineages, in particular between embryonic and extra-embryonic cell types?
• To what extent variation in residual activity from the inactive X affects cellular and tissular homeostasis and contributes to sex dimorphisms?

We combine stem cell lines analog of early development, integrated stem cell models (blastoids and models of implantation), comparative embryology in human and macaque embryos as well as interspecies chimeras in order to explore how and when dosage compensation is established in various primate species and the extent to which it is required for early embryogenesis. We use human organoids to visualize and measure X chromosome gene activity during differentiation of complex tissue-like structures. Our analyses include single cell approaches (single-cell RNA-seq, high-throughput RNA-FISH), CUT & RUN to assess chromatin remodeling and CRISPR-based screens.