Jean-Yves Coppee is managing the transcriptome and epigenome (PF2) platform. After a PhD in molecular biology (Universite de Louvain, Belgium), he spent 4 years at the “Centre de Génétique Moléculaire du CNRS” (head: Prof. P.P. Slonimski) working on the functional analysis of the yeast genome. He then joined the “Unité de Régulation de l’Expression Génétique” (headed by Antoine Danchin) at the Institut Pasteur where he used proteomics to study sulfur metabolism in Bacillus subtilis. Since 2000, he is responsible for the PF2 platform which is dedicated to the development and use of high throughput approaches (initially DNA arrays and since 2009 Next Generation Sequencing) for gene expression profiling.
Training: analysis of the transcriptome by RNAseq
The Transcriptome and Epigenome platform of the Biomics pole is organizing a one week (October 10, 2016 – October 14, 2016) training session dedicated to the analysis of the transcriptome by RNAseq. It is […]
Deciphering dormancy in Cryptocococcus neoformans
Cryptococcus neoformans is a sugar-coated yeast that is able to interact closely with numerous organisms in the environment including amebae, paramecium of nematodes. The interaction with these organisms probably shaped its virulence. The ability […]
Deciphering the virulence factors of Mycobacterium abscessus activated in the presence of environmental amoebae
Mycobacterium abscessus (M. abs) is an emerging pathogen causing lung infections in cystic fibrosis patients. Although the environmental reservoir of M. abs is currently unknown, M. abs possesses a gene pool dedicated to a […]
Transcriptome of different quiescence sub-states of neural stem cells in adult zebrafish
Vertebrate adult neural stem cells (NSCs) are generally quiescent, and the frequency of their cell cycle re-entry (“activation”) conditions their lifespan. Little is known of the molecular pathways controlling the NSC quiescence/activation balance. We […]
The role of lncRNA H19 in Thymopoiesis
“The thymus is a specialized organ that provides a unique environment for T cell development and differentiation. The study the thymus-settling progenitors (TSPs) and how they differentiate is important for the characterization of the […]
Private: Understanding translation fidelity in yeast
Externe collaboration with Genomic, Structure and Translation team of Olivier Namy Translation fidelity is essential for the correct decoding of genetic information. However, translation fidelity is not maximal, and several genes use alternative […]
Gene expression profiling in germinal center B cells
Germinal centers (GC) are essential for an effective humoral immune response. The GC provides an environment that stimulates B cells to proliferate in response to antigens and accumulate somatic mutations in immunoglobulin (Ig) genes, […]
Characterization of the SigmaS network by RNA sequencing and identification of SigmaS-controlled small regulatory RNAs in Salmonella
We have used directional RNA-sequencing and complementary assays to explore the SigmaS-dependent transcriptome of Salmonella enterica serovar Typhimurium. This study confirms the large regulatory scope of SigmaS and provides insights into its physiological functions […]
Escherichia coli transcriptomic analysis upon OmrA or OmrB overexpression
OmrA and OmrB are two small regulatory RNAs (sRNAs) conserved in enterobacteria. Their transcription is activated by the EnvZ-OmpR two-component system and their levels therefore increase in response to an increase in osmolarity. They […]
Intracellular membrane proliferation in E. coli
Overproduction of membrane proteins in the E. coli strains generally induce cell death. The multiple mutant C43 (DE3) derivative of BL21 (DE3) strain was selected to resist this overproduction. In this mutant, the membrane […]
A personal database system for large scale quantitative results exploration (Cassandre, PTR 463)
Cassandre is a project of personal database system, integrating a “user-friendly” interface to manage and explore multiple sets of large-scale experimental results in biology. Large-scale experiments that generate quantitative data, such as changes in […]
HIV signature on RIG-I-like receptors
The pathogenesis of HIV infection, and in particular the development of immunodeficiency, remains incompletely understood. During HIV infection both innate and adaptive immune responses are raised, but they appear to be insufficient or too […]
Role of neuronal, microglial and glial cells during rabies virus infection in the modulation of innate immune response: MIME-RAB
Rabies is an untreatable disease of humans due to lyssaviruses and Rabies virus (RABV) in particular. RABV is a highly neurotropic virus which prevent inflammation during the early phase of infection. In the brain, […]
Dynamic regulation of chromatin and transcription by HP1 Heterochromatin Proteins in relationship with RNA.
The three HP1 (Heterochromatin Protein 1), HP1a, HP1b, and HP1g proteins are epigenetic markers of heterochromatin, the condensed, repressed form of chromatin. They are typically known to associate to the di-/tri-methylated lysine 9 of […]
Biostatistics for data analysis
The platform provides statistical analyses of RNA-seq count data. Before any project starts, we help the user to design his experiment in order to ensure that it really addresses the biological question he wishes […]
The platform also has important technological and bibliographical survey activities for the wet lab as well as for the dry lab. Over the last months, the platform has established methods for the transcriptome sequencing […]
Régulation transcriptionnelle par l’Enhancer de Trithorax et Polycomb Corto et la Protéine Ribosomique L12.
Il est aujourd’hui connu que les protéines ribosomiques ont des fonctions extra-ribosomiques, et qu’en particulier, certaines d’entre elles contrôlent la transcription. Nous avons montré que, chez la drosophile, RPL12 interagit avec le facteur épigénétique […]
2020BAHD1 haploinsufficiency results in anxiety-like phenotypes in male mice, PLoS ONE 2020;15(5):e0232789.
2020Intracellular Staphylococcus aureus persisters upon antibiotic exposure, Nat Commun 2020 May;11(1):2200.
2020Transcytosis subversion by M cell-to-enterocyte spread promotes Shigella flexneri and Listeria monocytogenes intracellular bacterial dissemination, PLoS Pathog. 2020 Apr;16(4):e1008446.
2020Insights into amebiasis using a human 3D-intestinal model, Cell. Microbiol. 2020 Mar;:e13203.
2019Mycobacterium abscessus virulence traits unraveled by transcriptomic profiling in amoeba and macrophages, PLoS Pathog. 2019 Nov;15(11):e1008069.
2019Non-specific interference of cobalt with siderophore-dependent iron uptake pathways, Metallomics 2019 Nov;11(11):1937-1951.
2019Transcriptional profiling of a laboratory and clinical Mycobacterium tuberculosis strain suggests respiratory poisoning upon exposure to delamanid, Tuberculosis (Edinb) 2019 Jul;117:18-23.
2018checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes, Bioinformatics, 2018.
2018Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries, Nucleic Acids Res. 2018 07;46(12):6271-6284.
2018Enteric bacteria boost defences against oxidative stress in Entamoeba histolytica, Sci Rep 2018 Jun;8(1):9042.
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