dachshund Potentiates Hedgehog Signaling during Drosophila Retinogenesis

Proper organ patterning depends on a tight coordination between cell proliferation and differentiation. The patterning of Drosophila retina occurs both very fast and with high precision. This process is driven by the dynamic changes in signaling activity of the conserved Hedgehog (Hh) pathway, which coordinates cell fate determination, cell cycle and tissue morphogenesis. Here we show that during Drosophila retinogenesis, the retinal determination gene dachshund (dac) is not only a target of the Hh signaling pathway, but is also a modulator of its activity. Using developmental genetics techniques, we demonstrate that dac enhances Hh signaling by promoting the accumulation of the Gli transcription factor Cubitus interruptus (Ci) parallel to or downstream of fused. In the absence of dac, all Hh-mediated events associated to the morphogenetic furrow are delayed. One of the consequences is that, posterior to the furrow, dac- cells cannot activate a Roadkill-Cullin3 negative feedback loop that attenuates Hh signaling and which is necessary for retinal cells to continue normal differentiation. Therefore, dac is part of an essential positive feedback loop in the Hh pathway, guaranteeing the speed and the accuracy of Drosophila retinogenesis.MINECO Spain grants: (BFU2012-34324, BFU2015- 66040); Research Foundation—Flanders FWO grants: (G.0640.13, G.0791.14, PhD fellowship); Fundação para a Ciência e Tecnologia grant: (IF/01031/2012)

Cortical Neurogenesis Requires Bcl6-Mediated Transcriptional Repression of Multiple Self-Renewal-Promoting Extrinsic Pathways.

During neurogenesis, progenitors switch from self-renewal to differentiation through the interplay of intrinsic and extrinsic cues, but how these are integrated remains poorly understood. Here, we combine whole-genome transcriptional and epigenetic analyses with in vivo functional studies to demonstrate that Bcl6, a transcriptional repressor previously reported to promote cortical neurogenesis, acts as a driver of the neurogenic transition through direct silencing of a selective repertoire of genes belonging to multiple extrinsic pathways promoting self-renewal, most strikingly the Wnt pathway. At the molecular level, Bcl6 represses its targets through Sirt1 recruitment followed by histone deacetylation. Our data identify a molecular logic by which a single cell-intrinsic factor represses multiple extrinsic pathways that favor self-renewal, thereby ensuring robustness of neuronal fate transition

Predictors of hospital discharge and mortality in patients with diabetes and COVID-19: updated results from the nationwide CORONADO study

AIMS/HYPOTHESIS: This is an update of the results from the previous report of the CORONADO (Coronavirus SARS-CoV-2 and Diabetes Outcomes) study, which aims to describe the outcomes and prognostic factors in patients with diabetes hospitalised for coronavirus disease-2019 (COVID-19). METHODS: The CORONADO initiative is a French nationwide multicentre study of patients with diabetes hospitalised for COVID-19 with a 28-day follow-up. The patients were screened after hospital admission from 10 March to 10 April 2020. We mainly focused on hospital discharge and death within 28 days. RESULTS: We included 2796 participants: 63.7% men, mean age 69.7 ± 13.2 years, median BMI (25th-75th percentile) 28.4 (25.0-32.4) kg/m(2). Microvascular and macrovascular diabetic complications were found in 44.2% and 38.6% of participants, respectively. Within 28 days, 1404 (50.2%; 95% CI 48.3%, 52.1%) were discharged from hospital with a median duration of hospital stay of 9 (5-14) days, while 577 participants died (20.6%; 95% CI 19.2%, 22.2%). In multivariable models, younger age, routine metformin therapy and longer symptom duration on admission were positively associated with discharge. History of microvascular complications, anticoagulant routine therapy, dyspnoea on admission, and higher aspartate aminotransferase, white cell count and C-reactive protein levels were associated with a reduced chance of discharge. Factors associated with death within 28 days mirrored those associated with discharge, and also included routine treatment by insulin and statin as deleterious factors. CONCLUSIONS/INTERPRETATION: In patients with diabetes hospitalised for COVID-19, we established prognostic factors for hospital discharge and death that could help clinicians in this pandemic period. TRIAL REGISTRATION: Clinicaltrials.gov identifier: NCT04324736

Approches in silico et in vivo pour l'étude de la régulation transcriptionnelle : application à la cardiogenèse chez D. melanogaster

Au cours de ma thèse, je me suis intéressée au développement du système cardio-vasculaire chez la drosophile afin de mieux comprendre la logique de régulation de ce processus. Au cours de l'embryogenèse, la cardiogenèse est réalisée grâce à un réseau de régulation génique (GRN) qui conduit à la formation d'un simple tube cardiaque linéaire. Ensuite, lors de la métamorphose, le tube cardiaque larvaire est remodelé pour former l'organe adulte.J'ai d'abord participé à l'évaluation et à l'amélioration d'une nouvelle méthode, cisTargetX, qui permet prédire des modules cis-régulateurs (CRM) présentant des caractéristiques communes à un groupe de gènes co-exprimés.En utilisant cette méthode, j'ai analysé le transcriptome du remodelage du cœur afin de prédire des motifs pouvant être liés par des TF impliqués dans le contrôle temporel de l'expression des gènes, ainsi que les CRM associés. Grâce aux validations in-vivo des CRM prédits, j'ai démontré qu'ils étaient capables de reproduire le patron d'expression temporel attendu. J'ai également démontré que la mutation du motif en question au sein de deux des CRM testés permet de supprimer son patron d'expression sauvage. Ce motif est reconnu par des facteurs de transcription (TF) de la famille des récepteurs nucléaires (NR). Dhr3, un NR fortement exprimé au début de l'induction des gènes analysés, est montré comme étant essentiel au patron d'expression temporel. Nos résultats suggèrent une architecture du GRN, dans lequel les régulations temporelle et spatiale sont distinctes.Par la suite, j'ai participé à la caractérisation du GRN impliqué dans la cardiogenèse. En combinant un transcriptome issu de la différenciation des cellules cardiaques avec des expériences ChIP-on-Chip sur le TF MEF2, j'ai prédit que certains TF appartenant aux familles bZIP et REL sont susceptibles de participer au GRN responsable de la différenciation cardiaque. La validation in-vivo de ces prédictions est en cours.During my thesis, I focused on the development of the cardiovascular system in Drosophila in order to investigate the regulatory logic of this process. During embryogenesis, cardiogenesis is mediated by a gene regulatory network which includes conserved signaling pathways and transcription factors, and leads to the formation of a linear cardiac tube. Then, during metamorphosis, the larval cardiac tube is remodeled to form the adult organ.I first participated in the evaluation and the improvement of a new method, cisTargetX, that uses a comprehensive library of motifs, combined with phylogenetic conservation, to identify potential cis-regulatory modules (CRM) presenting common features in a cluster of co-expressed genes.Using this method among other tools, I analysed cardiac remodeling during metamorphosis to predict motifs for transcription factors (TF) involved in the temporal control of gene expression, and also their associated CRM. I performed in-vivo validations of predicted CRM, and demonstrated that they reproduce the expected temporal expression pattern. In addition, I demonstrated that motifs mutation within selected CRM abrogate this expression pattern. This motif is predicted to be recognized by a TF that belong to the nuclear receptor (NR) family. Dhr3, a NR highly expressed at the onset of the induction of the analysed gene set, is demonstrated to be essential for CRM temporal pattern. Our results suggest a modular architecture of the regulatory machinery, in which the temporal and spatial regulations are distinct.Next, I participated in the characterization of the Gene Regulatory Network (GRN) involved in cardiac differentiation during embryogenesis. Combining transcriptome profiling of differentiating cardiac cells with Mef2 Chip-on-Chip experiments allowed me to predict that TF belonging to bZIP and REL family are likely to participate in the GRN driving cardiac differentiation. In-vivo validation of these predictions is in progress

Devenir du prion dans les sols (rôle des micro-organismes protéolytiques)

L'étude du devenir de la protéine du prion dans les sols est nécessaire en raison de la possible contamination de ces sols par l'agent infectieux des Encéphalopathies Spongiformes Transmissibles. L'objectif principal de ce travail était d'évaluer la capacité des microorganismes telluriques à dégrader une protéine du prion produite par recombinaison(recPrP b). La dynamique de l'activité protéolytique a été suivie dans le sol après ajout de matière organique animale de complexité croissante (caseine, broyat de cervelle d'agneau, carcasses). Nous avons mis en évidence une augmentation rapide de l'activité protéolytique s'accompagnant d'un enrichissement en bactéries appartenant au genre Bacillus. L'existence d'enzymes protéolytiques capables de dégrader la recPrP b in vitro et dans le sol a été montrée. Cette étude apporte des éléments qui pourraient contribuer à limiter la persistance du prion dans les sols, et qui sont à prendre en compte dans la gestion du risque prion dans les solsBecause soil can be contaminated with the infectious agent of the Transmissible Spongiform Encephalopathies, study of the fate of the prion in soil has to be studied. our objective was to evaluate the ability of soil microorganisms to degrade a recombinant prion proten (b recPrP). The temporal dynamics of soil proteolytic activity was monitored following an input animal organic matter of increased complexity (casein, lamb brain, buried carcasses). We showed that soil proteolytic activity was rapidly stimulated, with an enrichment of bacterial community with Bacillus sp. Proteolytic enzymes participating to the degradation of recPrP b in vitro and in soil were revealed. This study brought to the factors which could contribute to limit the persistence of the prion in soil, and which has to take into account in the soil contamination managementLYON1-BU.Sciences (692662101) / SudocSudocFranceF

Integrative analysis of regulatory tracks for the identification of direct TF-target interactions

status: accepte

Identification of lineage-specific Cis-regulatory modules associated with variation in transcription factor binding and chromatin activity using Ornstein-Uhlenbeck models

Scoring the impact of noncoding variation on the function of cis-regulatory regions, on their chromatin state, and on the qualitative and quantitative expression levels of target genes is a fundamental problem in evolutionary genomics. A particular challenge is how to model the divergence of quantitative traits and to identify relationships between the changes across the different levels of the genome, the chromatin activity landscape, and the transcriptome. Here, we examine the use of the Ornstein-Uhlenbeck (OU) model to infer selection at the level of predicted cis-regulatory-modules (CRMs), and link these with changes in transcription factor binding and chromatin activity. Using publicly available cross-species ChIP-Seq and STARR-Seq data we show how OU can be applied genome-wide to identify candidate transcription factors for which binding site and CRM turnover is correlated with changes in regulatory activity. Next, we profile open chromatin in the developing eye across three Drosophila species. We identify the recognition motifs of the chromatin remodelers, Trithorax-like and Grainyhead as mostly correlating with species-specific changes in open chromatin. In conclusion, we show in this study that CRM scores can be used as quantitative traits and that motif discovery approaches can be extended towards more complex models of divergence

Les groupes d’enseignement facultaire : un outil adapté à l’approche par compétences

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