DNA Micro-arrays  


  HEADDr Coppee Jean-Yves / jycoppee@pasteur.fr
  MEMBERSDr Coppee, Jean-Yves / Dr Barthelemy, Mathieu / Dr Dillies, Marie-Agnès / Haury, Anne-Claire / Sismeiro, Odile / Proux, Caroline / Soubigou, Guillaume


  Annual Report

The DNA microarray platform (PF2) is dedicated to the development of microarrays for gene expression profiling of model microorganisms and pathogens. The platform also deals with studies centered on higher eukaryotes. Various technologies are available at the platform : home made spotted arrays and commercial arrays (Agilent, Nimblegen and Affymetrix arrays). In mid 2008, the Pasteur Genopole has acquired a next generation sequencing machine (Illumina Genome Analyzer) which allows the production of millions of 35 bp reads in a single run. High throughput sequencing is replacing the array approach for some applications such as small RNA profiling, analysis of DNA-protein interactions (studying regulatory protein binding and exploring chromatin packaging), annotation of full transcriptomes.

In 2008, the platform has been involved in more than 20 projects. These projects are mainly long-term (several months to years) collaborations with Pasteurian research units. The platform is also collaborating with teams from the International Network of Pasteur Institutes and has established collaborations with several non-Pasteurian teams.

The complete list of all these projects is available on the website of the platform. The projects centered on model microorganisms and pathogens notably concern Legionella pneumophila, Entamoeba histolytica, Plasmodium, Mycobacterium smegmatis, Mycobacterium abscessus. The projects dedicated to higher eukaryotes mainly concern Homo sapiens, Mus musculus and Drosophila melanogaster.

These projects aim at answering the following biological questions:

- study of virulence factors

- inter-species transcriptome comparisons

- study of host-pathogen interactions

- study of the effects of environmental pressures (stress, immune pressure, drug pressure...) on the pathogen

- identification of regulator targets (virulence, motility...)

- host response to infection, developmental biology, oncogenesis

The platform is in charge of the preparation of the arrays (probes design, spotting if needed) as well as of training for the use of the arrays and analysis of results. For the projects based on the Affymetrix technology, the PF is also in charge of labelling and hybridization reactions. Data analysis and handling represent 50 % of the activities of the platform. Several tools allowing normalization of the data and their statistical analysis are developped and installed at the platform. We are essentially working with the R environment (Bioconductor) and with several commercial softwares for data mining and interpretation.

All equipments and softwares needed for the use and the analysis of the chips are freely accessible for the whole campus. This functioning mode allows the development of strong interactions between the PF and the teams with which we are collaborating.

The platform also has some training activities. In 2008, we have participated to several Pasteur Courses (Molecular and Cellular Genetics, Protein Biochemistry)

The PF also exerts a bibliographical and technical survey activity (wet and dry lab) so to rapidly integrate all the technological improvements and new applications of this technology.

Keywords: DNA arrays, transcriptomics, epigenomics, data analysis, next generation sequencing



  Publications

Natalang O, Bischoff E, Deplaine G, Proux C, Dillies MA, Sismeiro O, Guigon G, Bonnefoy S, Patarapotikul J, Mercereau-Puijalon O, Coppee JY, David PH.

2008

Dynamic RNA profiling in Plasmodium falciparum synchronized blood stages exposed to lethal doses of artesunate.

BMC Genomics, 9(1):388


Labalette C, Nouët Y, Levillayer F, Armengol C, Renard CA, Soubigou G, Xia T, Buendia MA, Wei Y.

2008

The LIM-only protein FHL2 mediates ras-induced transformation through cyclin D1 and p53 pathways.

PLoS ONE, 3(11):e3761


Blazquez S, Guigon G, Weber C, Syan S, Sismeiro O, Coppée JY, Labruyère E, Guillén N.

2008

Chemotaxis of Entamoeba histolytica towards the pro-inflammatory cytokine TNF is based on PI3K signalling, cytoskeleton reorganization and the Galactose/N-acetylgalactosamine lectin activity

Cell Microbiol., 10(8):1676-86


Tien MT, Girardin SE, Regnault B, Le Bourhis L, Dillies MA, Coppée JY, Bourdet-Sicard R, Sansonetti PJ, Pédron T.

2006

Anti-inflammatory effect of Lactobacillus casei on Shigella-infected human intestinal epithelial cells.

J Immunol., 176(2):1228-37.


Brüggemann H, Hagman A, Jules M, Sismeiro O, Dillies MA, Gouyette C, Kunst F, Steinert M, Heuner K, Coppée JY, Buchrieser C.

2006

Virulence strategies for infecting phagocytes deduced from the in vivo transcriptional program of Legionella pneumophila.

Cell Microbiol., 8(8):1228-40.



  Web Site

More informations on our web site




Activity Reports 2009 - Institut Pasteur
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