Gene Expression and Development Group Research

How does any cell control gene expression? How is gene expression integrated in a whole multicellular organism? What happens when these regulations fail? Are human pathologies linked to defective controls of gene expression? These longstanding issues are far from solved. We focus on the controls of gene expression exerted at the RNA level. While it was initially thought that gene expression was mainly regulated at the DNA level (transcriptional controls), it is now clear that RNA-centered regulations ("post-transcriptional regulations") are instrumental.
The "Gene Expression and Development" (GED) team endavours to decipher how post-transcriptional regulations contribute to vertebrate development, using mice and frogs (Xenopus: why Xenopus?) as models, with strong impacts for human health.

Specific goals

CELF1-linked diseases

CELF1 is an RNA-binding protein that controls several aspects of RNA fate (alternative splicing, translation, decay). In human, it is involved in a genetic disease named Myotonic, dystrophy, type I (DM1). We developed Celf1-disrupted mice, which proved valuable models to study DM1. We also demonstrated the developmental functions of CELF1 in vertebrate somite segmentation, or mammalian male gametogenesis.

Figure 1. Why are Celf1-disrupted males sterile? While the epididimes of wild-type mouse males  essentially contain spermatozoa (A), those of Celf1-null males essentially contain round cells (B), corresponding to immature spermatids prematuraly released from the seminiferous tubules. This spermiogenesis defect arises from low testosterone and high aromatase activity, and can be treated with exogenous testosterone or the aromatase inhibitor Letrozole (C). Other data reveal that theCELF1 RNA-binding protein directy represses the translation of aromatase RNA, indicating a direct function of CELF1 in controlling hormonal status. (See : Boulanger et al, MCB 2015, for details).

We are currently studying the physiopathological functions of CELF1 in lens biology and disease (cataracts) and Alzheimer disease.

Epidermis stability

We have recently shown that the RNA-binding proteins Ptbp1 and Esrp1, as well as the RNA exosome component Exosc9, were involved in Xenopus epidermis stability. Esrp1 positively controls ptbp1 expression, and the pathways linking Esrp1/Ptbp1 and Exosc9 to epidermis stability are different. The embryos depleted in Ptbp1, Esrp1 or Exosc9 have dorsal "blisters", which are reminiscent of some human genodermatoses (inherited skin diseases).

Figure 3. The "blister" phenotype. Xenopus embryos are excellent models for reverse genetics approaches. As exemples, we show here a control (non-injected, NI) Xenopus embryo, as well  as embryos previously injected with molecular tools aimed at blocking the expression of specific  genes (morpholino antisense oligoncleotides, Mo). Embryos injected with morpholinos directed  ptbp1, exosc9 or esrp1 all display characteristic "bubbles" or "blisters" on the dorsal fin. Since  these three genes encode post-transcriptional regulators of gene expression, these data illustrate  a link between skin stability and post-transcriptional controls.

Xenopus embryos epidermis is a simple model of pluristratified epidermis. It includes only four cell types, which express specific markers.

Figure 2. Xenopus larvae as models of vertebrate epithelium development. Shown are representative in situ hybridizations with the indicated probes, which depict the variety of  cell types in Xenopus embryo epidermis.

To tackle the links between post-transcriptional controls and epidermis stability, we integrate high-throughput genomics with reverse genetics and phenotype analyses. Genomic approaches include deep RNA sequencing and CLIPseq to systematically identify the RNA ligands of RNA-binding protein. Reverse genetics is carried out in Xenopus with antisense Morpholino oligonucleotides and CRISPR/Cas9 genome editing.

 

Figure 4. Deep RNA sequencing to uncover RNA splicing defects in Xenopus embryos. The  reads obtained by deep sequencing of RNA extracted from control embryos (red), embryos  injected with the Exosc9 morpholino (blue) or the ptbp1 morpholino (green) were mapped on the  Xenopus genome. We show here a particular exon (circled red), that is present within the  mRNA in ptbp1 morpholino-injected embryos, but absent in the two oher samples. This reveals  that the RNA-binding Ptbp1 directly or indirectly represses the inclusion of this exon.

Transversal goals

Because developmental defects are at the origin of an impressive number of human pathologies, we continuously endeavour to link our findings to human health.

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