Aitor González

Intronic delay is essential for oscillatory expression in the segmentation clock

Proper timing of gene expression is essential for many biological events, but the molecular mechanisms that control timing remain largely unclear. It has been suggested that introns contribute to the timing mechanisms of gene expression, but this hypothesis has not been tested with natural genes. One of the best systems for examining the significance of introns is the oscillator network in the somite segmentation clock, because mathematical modeling predicted that oscillating expression depends on negative feedback with a delayed timing. The basic helix–loop–helix repressor gene Hes7 is cyclically expressed in the presomitic mesoderm (PSM) and regulates the somite segmentation. Here, we found that introns lead to an ∼19-min delay in the Hes7 gene expression, and mathematical modeling suggested that without such a delay, Hes7 oscillations would be abolished. To test this prediction, we generated mice carrying the Hes7 locus whose introns were removed. In these mice, Hes7 expression did not oscillate but occurred steadily, leading to severe segmentation defects. These results indicate that introns are indeed required for Hes7 oscillations and point to the significance of intronic delays in dynamic gene expression.

MicroRNA9 regulates neural stem cell differentiation by controlling Hes1 expression dynamics in the developing brain.

Earlier studies show that Hes1 expression is oscillatory in neural stem cells but sustained and high in the roof plate and the floor plate, and that such different dynamics of Hes1 expression (oscillatory versus sustained) regulate different proliferation and differentiation characteristics of these cells (active in neural stem cells but rather dormant in roof/floor plate cells). The mechanism of how different dynamics of Hes1 expression is controlled remains to be determined. Here, we found that the seed sequence of microRNA‐9 (miR‐9) is complementary to the 3′‐UTR sequence of Hes1 mRNA. MiR‐9 is highly expressed in the ventricular zone of the developing brain, which contains neural stem cells, but it is not expressed in the roof plate or the floor plate. Over‐expression of miR‐9 negatively regulates the Hes1 protein expression by interacting with the 3′‐UTR of Hes1 mRNA, thereby inducing cell cycle exit and neuronal differentiation. Conversely, knockdown of miR‐9 inhibits neuronal differentiation. Furthermore, knockdown of miR‐9 inhibits the oscillatory expression of Hes1 mRNA in neural stem cells. These results indicate that miR‐9 regulates the proliferation and differentiation of neural stem cells by controlling the dynamics of Hes1 expression in the developing brain.

Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc

MOTIVATIONS The development of most tissues and organs relies on a limited number of signal transduction pathways enabling the coordination of cellular differentiation. A proper understanding of the roles of signal transduction pathways requires the definition of formal models capturing the main qualitative features of these patterning processes. This is a challenging task because the underlying processes, diffusion, regulatory modifications, reception and sequestration of signalling molecules, transcriptional regulation of target genes, etc. are only partly characterized. In this context, qualitative models can be more readily proposed on the basis of available (molecular) genetic data. But this requires novel computational tools and proper qualitative representations of phenomena such as diffusion or sequestration. To assess the power and limits of a logical formalism in this context, we propose a multi-level model of the multi-cellular network involved in the definition of the anterior-posterior boundary during the development of the wing disc of Drosophila melanogaster. The morphogen Hedgehog (Hh) is the inter-cellular signal coordinating this process. It diffuses from the posterior compartment of the disc to activate its pathway in cells immediately anterior to the boundary. In these boundary cells, the Hh gradient induces target genes in distinct domains as a function of the Hh concentration. One target of Hh signalling is the gene coding for the receptor Patched (Ptc), which sequesters Hh and impedes further diffusion, thereby refining the boundary. RESULTS We have delineated a logical model of the patterning process defining the cellular anterior-posterior boundary in the developing imaginal disc of Drosophila melanogaster. This model qualitatively accounts for the formation of a gradient of Hh, as well as for the transduction of this signal through a balance between the activatory (CiA) and inhibitory (CiR) products of the gene cubitus interruptus (ci). Wild-type and mutant simulations have been carried out to assess the coherence of the model with experimental data. Interestingly, our computational analysis provides novel insights into poorly understood processes such as the regulation of Ptc by CiR, the formation of a functional gradient of CiA across boundary cells, or yet functional En differences between anterior and posterior cells. In conclusion, our model analysis demonstrates the flexibility of the logical formalism, enabling consistent qualitative representation of diffusion, sequestration and post-transcriptional regulatory processes within and between neighbouring cells. AVAILABILITY An XML.le containing the proposed model together with annotations can be downloaded from our website (http://gin.univ-mrs.fr/GINsim/), along with GINsim, a logical modelling and simulation software freely available to academic groups.

Oscillatory gene expression and somitogenesis

A bilateral pair of somites forms periodically by segmentation of the anterior ends of the presomitic mesoderm (PSM). This periodic event is regulated by a biological clock called the segmentation clock, which involves cyclic gene expression. Expression of her1 and her7 in zebrafish and Hes7 in mice oscillates by negative feedback, and mathematical models have been used to generate and test hypotheses to aide elucidation of the role of negative feedback in regulating oscillatory expression. her/Hes genes induce oscillatory expression of the Notch ligand deltaC in zebrafish and the Notch modulator Lunatic fringe in mice, which lead to synchronization of oscillatory gene expression between neighboring PSM cells. In the mouse PSM, Hes7 induces coupled oscillations of Notch and Fgf signaling, while Notch and Fgf signaling cooperatively regulate Hes7 oscillation, indicating that Hes7 and Notch and Fgf signaling form the oscillator networks. Notch signaling activates, but Fgf signaling represses, expression of the master regulator for somitogenesis Mesp2, and coupled oscillations in Notch and Fgf signaling dissociate in the anterior PSM, which allows Notch signaling‐induced synchronized cells to express Mesp2 after these cells are freed from Fgf signaling. These results together suggest that Notch signaling defines the prospective somite region, while Fgf signaling regulates the pace of segmentation. It is likely that these oscillator networks constitute the core of the segmentation clock, but it remains to be determined whether as yet unknown oscillators function behind the scenes. WIREs Dev Biol 2012 doi: 10.1002/wdev.46

Aging Alters Histone H4 Acetylation and CDC2A in Mouse Germinal Vesicle Stage Oocytes

The reproductive potential of mammals decreases with aging, until reaching infertility. One reason for aging-related infertility is the decrease of the reproductive capability of old oocytes. It was found previously that gene expression, histone acetylation, and protein function are altered by aging in metaphase II (MII) stage oocytes. MII oocytes develop from germinal vesicle (GV)-stage oocytes. Here, we hypothesized that the defects of old MII oocytes arise at the GV stage. To prove this hypothesis, we examined the acetylations of histone H4 at lysines 5 (H4K5), 8 (H4K8), 12 (H4K12), and 16 (H4K16) in old GV and MII oocytes. We found that acetylation of H4K12 and H4K16 decreased in old GV oocytes. Acetylation of H4K12 later increased in old MII oocytes. We also examined expression of Cdc2a, a gene related to H4K12 acetylation. Cdc2a expression increased in old nonsurrounded nucleolus (NSN) oocytes but decreased in old MII oocytes. On the other hand, the protein and kinase activities of CDC2A decreased in both GV and MII old oocytes. Finally, we showed that correction of the histone deacetylation of old oocytes at the GV stage restores younglike levels of H4K12 acetylation and CDC2A protein at the MII stage. These data support our hypothesis that abnormalities of histone acetylation at the GV stage are the cause of alterations at the MII stage. Our study provides evidence for strategies targeting the GV stage of oocytes to overcome aging-induced infertility.

Dynamical analysis of the regulatory network defining the dorsal-ventral boundary of the Drosophila wing imaginal disc

The larval development of the Drosophila melanogaster wings is organized by the protein Wingless, which is secreted by cells adjacent to the dorsal–ventral (DV) boundary. Two signaling processes acting between the second and early third instars and between the mid- and late third instar control the expression of Wingless in these boundary cells. Here, we integrate both signaling processes into a logical multivalued model encompassing four cells, i.e., a boundary and a flanking cell at each side of the boundary. Computer simulations of this model enable a qualitative reproduction of the main wild-type and mutant phenotypes described in the experimental literature. During the first signaling process, Notch becomes activated by the first signaling process in an Apterous-dependent manner. In silico perturbation experiments show that this early activation of Notch is unstable in the absence of Apterous. However, during the second signaling process, the Notch pattern becomes consolidated, and thus independent of Apterous, through activation of the paracrine positive feedback circuit of Wingless. Consequently, we propose that appropriate delays for Apterous inactivation and Wingless induction by Notch are crucial to maintain the wild-type expression at the dorsal–ventral boundary. Finally, another mutant simulation shows that cut expression might be shifted to late larval stages because of a potential interference with the early signaling process.

Hes1 in the somatic cells of the murine ovary is necessary for oocyte survival and maturation

The Notch pathway plays an important role in ovary development in invertebrates like Drosophila. However its role for the mammalian ovary is unclear. Mammalian Hes genes encode transcriptional factors that mediate many of the activities of the Notch pathway. Here, we have studied the function of Hes1 during embryonic development of the mouse ovary. We find that Hes1 protein is present in somatic cells and oocyte cytoplasm and decreases between E15.5 and P0. Conventional Hes1 knock-out (KO), Hes1 conditional KO in the ovarian somatic, and chemical inhibition of Notch signaling decrease the total number, size and maturation of oocytes and increase the number of pregranulosa cells at P0. These defects correlate with abnormal proliferation and enhanced apoptosis. Expression of the proapoptotic gene Inhbb is increased, while the levels of the antiapoptotic and oocyte maturation marker Kit are decreased in the Hes1 KO ovaries. Conversely, overactivation of the Notch pathway in ovarian somatic cells increases the number of mature oocytes and decreases the number of pregranulosa cells. Fertility is also reduced by either Hes1 deletion or Notch pathway overactivation. In conclusion, our data suggest that the Notch-Hes1 pathway regulates ovarian somatic cell development, which is necessary for oocyte survival and maturation.

Control of Hes7 expression by Tbx6, the Wnt pathway and the chemical Gsk3 inhibitor LiCl in the mouse segmentation clock.

The mouse segmentation is established from somites, which are iteratively induced every two hours from the presomitic mesoderm (PSM) by a system known as the segmentation clock. A crucial component of the segmentation clock is the gene Hes7, which is regulated by the Notch and Fgf/Mapk pathways, but its relation to other pathways is unknown. In addition, chemical alteration of the Wnt pathway changes the segmentation clock period but the mechanism is unclear. To clarify these questions, we have carried out Hes7 promoter analysis in transgenic mouse embryos and have identified an essential 400 bp region, which contains binding sites of Tbx6 and the Wnt signaling effector Lef1. We have found that the Hes7 promoter is activated by Tbx6, and normal activity of the Hes7 promoter in the mouse PSM requires Tbx6 binding sites. Our results demonstrate that Wnt pathway molecules activate the Hes7 promoter cooperatively with Tbx6 in cell culture and are necessary for its proper expression in the mouse PSM. Furthermore, it is shown that the chemical Gsk3 inhibitor LiCl lengthens the oscillatory period of Hes7 promoter activity. Our data suggest that Tbx6 and the Wnt pathway cooperatively regulate proper Hes7 expression. Furthermore, proper Hes7 promoter activity and expression is important for the normal pace of oscillation.

Automatic reconstruction of the mouse segmentation network from an experimental evidence database

Mammalian vertebrae, ribs, body wall musculature and back skin develop from repetitive embryonic tissues called somites. The development of somites depends on the molecular oscillations of the products of so-called cyclic genes. The underlying network involves the Wnt, Fgf/Mapk, Notch signaling pathways and the T-box genes. The discovery of this network is based on genetic interactions. Because of regulatory feedbacks and cross-regulation between pathways, it is often difficult to intuitively identify direct molecular interactions underlying genetic interactions. To address this problem, we developed a method based on a database and graph theory algorithms. We first encoded genetic and non-genetic experiments in a relational database. Next, we built a reference network with the data from non-genetic experiments and the KEGG pathway database. Then, we computed the shortest path between the nodes for each genetic interaction in the reference network to propose direct molecular interactions. The resulting network is the largest computational representation of the mammalian segmentation network to date with 36 nodes and 57 interactions. In some instances, a number of genetic interactions could be explained by adding a single link to the reference network, which leads to experimentally testable hypotheses. Two examples of such predictions are the direct transcriptional regulation of Dll3 and Fgf8 genes by the Rbpj and Ctnnb1 products, respectively. Furthermore, the computed shortest paths suggest that cross-talks from the Wnt to the Fgf/Mapk and Notch pathways might be mediated by the Dvl genes. This method can be applied in any system where gene expression changes are observed as a response to some gene perturbation, for instance in cancer cells.

Hopf bifurcation in the presomitic mesoderm during the mouse segmentation

Vertebrae and ribs arise from embryonic tissues called somites. Somites arise sequentially from the unsegmented embryo tail, called presomitic mesoderm (PSM). The pace of somite formation is controlled by gene products such as hairy and enhancer of split 7 (Hes7) whose expression oscillates in the PSM. In addition to the cyclic genes, there is a gradient of fibroblast growth factor 8 (Fgf8) mRNA from posterior to anterior PSM. Recent experiments have shown that in the absence of Fgf signaling, Hes7 oscillations in the anterior and posterior PSM are lost. On the other hand, Notch mutants reduce the amplitude of posterior Hes7 oscillations and abolish anterior Hes7 oscillations. To understand these phenotypes, we delineated and simulated a logical and a delay differential equation (DDE) model with similar network topology in wild-type and mutant situations. Both models reproduced most wild-type and mutant phenotypes suggesting that the chosen topology is robust to explain these phenotypes. Numerical continuation of the model showed that even in the wild-type situation, the system changed from sustained to damped, i.e. a Hopf bifurcation occurred, when the Fgf concentration decreased in the PSM. This numerical continuation analysis further indicated that the most sensitive parameters for the oscillations are the parameters of Hes7 followed by those of Lunatic fringe (Lfng) and Notch1. In the wild-type, the damping of Hes7 oscillations was not so strong so that cells reached the new somites before they lose Hes7 oscillations. By contrast, in the fibroblast growth factor receptor 1 (Fgfr1) conditional knock-out (cKO) mutant simulation, Notch signaling was not able to maintain sustained Hes7 oscillations. Our analysis suggests that Fgf signaling makes cells enter an oscillatory state of Hes7 expression. After moving to the anterior PSM, where Fgf signaling is missing, Notch signaling compensates the damping of Hes7 oscillations in the anterior PSM.