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Genome regulation & evolution

Dr. Denis Dupuy

Research officer (CR1), Inserm


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Tel: +33(0)540008404


Denis Dupuy initially trained in Biology at University of Pau and got his Master of Science in Molecular and Cell Biology at Université Bordeaux Segalen. He did his Ph.D. thesis in human genetics in the laboratory of Dr. Benoit Arveiler at the University of Bordeaux (1998-2001) working on positional cloning of schizophrenia susceptibility gene. He then joined the group of Dr Marc Vidal, at the Dana-Farber Cancer Institute (Harvard Medical School, Boston, Ma) for a Post-Doctoral training in systems biology. There he acquired the tools and methods needed to perform systematic analysis of spatiotemporal gene expression in vivo in C. elegans.

Keys words / Expertise / Techniques

C. elegans, development, GFP, systems biology, bioinformatics, high throughput RNAi, in vivo, miRNA, splicing, post transcriptional regulation, evolution


The major goal of our group is to generate an integrative model of tissue-specific post-transcriptional regulation processes in Caenorhabditis elegans. Many cis-acting elements and trans-acting factors involved in the regulation of these processes have been characterized. However, integrative models of the molecular mechanisms underlying the sophisticated cell- and stage-specific patterns of regulation are yet to be developed due to difficulties in following these events in vivo. Post-transcriptional regulation represents a critical aspect of genetic regulatory networks in eukaryotes. To dissect the genetic requirements for these mechanisms we will generate the first quantitative genome-scale dataset of post-transcriptional regulation in vivo during C. elegans development.

Activity report

We focus our effort on two major aspects of post-transcriptional regulation and in particular the analysis of alternative splicing

Fig. 1: Two-color reporters for in-vivo post transcriptionalregulation studies

Alternative splicing of pre-mRNAs is a widespread mechanism that contributes to the spatiotemporal diversity of gene expression in metazoans. In Caenorhabditis elegans, it has been estimated that ~10% of genes are subjected to alternative splicing. To date, there is no information about global regulation of alternative splicing during worm development. In a recent study using a custom-made microarray, only ~20% of the tested genes showed a significant change in isoform ratio in the course of development. For the majority of the genes, for which EST data indicates alternative splicing events, no variation has been observed. This might indicate that most alternative isoforms are regulated in a tissue-specific rather than stage-specific manner. Such tissue- or cell-specific events are notoriously difficult to follow using microarray analyses. We will use a variation of the two-color reporter system pioneered by our collaborator H. Kuroyanagi (Tokyo) in which two fluorescent reporters are respectively fused to mutually exclusive alternatively spliced exons (Figure 1b), to characterize the alternative splicing patterns of 200 genes. This will provide the first large-scale overview of alternative splicing regulation in vivo in a metazoan organism.

In summary

To build dynamic models of cell differentiation it will be important to integrate comprehensive datasets of expression information and physical relationships between regulators and their targets within the system of interest. Tremendous efforts are underway to collect such datasets in C. elegans which make it the ideal model organism to reach this objective. Our goal is to complement these approaches with a systematic quantitative analysis of major spatiotemporal post-transcriptional regulation processes in vivo in C. elegans.

IGEM 2015

In 2012 D. Dupuy launched the first Bordeaux based team to participate in the International Genetically Engineered Machine (IGEM) competition. For the fourth participation a team of twenty eight students gathered every week for evening sessions of discussions and planning for a new synthetic biology project to be carried out over the summer. Fourteen undergraduate students represented the «Cured vine» project at the IGEM Giant Jamboree in Boston in September 2015 and were awarded a Gold medal in the Environment track.


Selected publications

  • Cornes E, Porta-De-La-Riva M, AristizĂĄbal-Corrales D, Brokate-Llanos AM, GarcĂ­a-RodrĂ­guez FJ, Ertl I, DĂ­az M, Fontrodona L, Reis K, Johnsen R, Baillie D, Muñoz MJ, Sarov M, Dupuy D, CerĂłn J. Cytoplasmic LSM-1 protein regulates stress responses through the insulin/IGF-1 signaling pathway in Caenorhabditis elegans. RNA 2015; 21 (9), 1544-1553
  • Marza E, Taouji S, Barroso K, Raymond AA, Guignard L, Bonneu M, Pallares‐Lupon N, Dupuy JW, Fernandez‐Zapico MX, Rosenbaum J, Palladino F, Dupuy D, Chevet E. Genome‐wide screen identifies a novel p97/CDC‐48‐dependent pathway regulating ER‐stress‐induced gene transcription EMBO reports. 2015; 16 (3), 332-340
  • Cornes E, QuĂ©rĂ© CAL, Giordano-Santini R, Dupuy D. Applying antibiotic selection markers for nematode genetics. Methods. 2014; 68(3) 403–408
  • Amrane S, Rebora K, Zniber I, Dupuy D, Mackereth CD. Backbone-independent nucleic acid binding by splicing factor SUP-12 reveals key aspects of molecular recognition, Nature Communications. 2014; 5: 4595

Research team

  • Dr. Denis DUPUY Team leader
  • Sabrina ROUSSEAU Engineer (IE, Inserm)
  • Jonathan MILLET PhD Student (Inserm-MNRT)
  • Eric CORNES PhD Student (University Pompeu Fabra)

This team is part of the unit “ARN: Regulation Naturelle et Artificielle” (ARNA), INSERM U869 (now U1212 since January 2016)

Institut Européen de Chimie et Biologie
2, Rue Robert Escarpit - 33607 PESSAC - France
Tel. : +33 (5) 40 00 30 38 - Fax. : +33 (5) 40 00 30 68
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