TD / TP bioinfo Techniques specific to repeated DNA analysis and  "Non-coding" RNAs

Cristina Vieira (Pr. Univ), Emmanuelle Lerat (CR1, CNRS)

Identification of repeats in the genome, model and non-model species. Presentation of tools and use of DNApipeTE with Galaxy. Quantification and differential analysis of small RNAs in population analysis. Presentation of tools and use of TEcount with Galaxy.

Please note: please bring a laptop with a WiFi card (no iPad-style tablets) to take advantage of bioinfo tutorials.

TP / TD bioinfo "Analysis and processing of data (BS-Seq, Me-DIP, ChIP-Seq)"

Christoph Grunau (Pr. Univ. Perpignan), Clémentine Vitte (CR1 CNRS, GQE-Le Moulon)

One afternoon will be dedicated to a hands-on bioinformatic analysis of Chip-seq and bisulfite-seq data. Using a model dataset from animals and plants (provided on site), users will have to control the quality of the sequencing data, map the reads to a reference genome, analyze the read counts, and detect genomic regions that are differentially enriched between two samples .

Please note: please bring a laptop with a WiFi card (no iPad-style tablets) to take advantage of bioinfo tutorials.

Conference / debate "  Historical and epistemological aspects of epigenetics  "

Francesca Merlin (CR2, CNRS-IHPST) & Antonine Nicoglou (PostDoc Labex “Who Am I?”, CRPMS & Institut Jacques Monod, IHPST)

This historico-philosophical introduction aims to clearly mark, on the one hand, the difference that must be made between epigenesis and epigenetics and, on the other hand, the link that can be made between the genealogy of epigenetics and the different traditions that derived from it and the way it is conceived today. We will thus show how the historical opposition of epigenesis to other theoretical currents, in particular preformationism, is also embodied in the biology of the twentieth century and in what sense today's epigenetics (which is forged since the 1970s) is a specific field of research, independent and independent of historical debates around epigenesis and its alternatives. The conference will take place in four stages. First, we will outline the history of epigenesis, from Aristotle until the end of the 19th century. Then, we will show in what forms the traditions of preformationism and epigenesis are embodied and still oppose in the twentieth century. In third place,  we will get to the heart of the matter, by analyzing the contemporary conceptions of epigenetics from the years 1970-80 until today, by distinguishing in particular the approaches which focus on the genetic relationship and development on the one hand and those that focus more on the link between “extended heredity” beyond genetic information alone and evolution on the other hand. Finally, we will identify and discuss the new philosophical problems and issues raised by epigenetics today, in particular in the fields of ecology and evolution.

TD / TP "  Molecular epigenetics techniques: which tools for which questions  and what species "

Stéphane Maury (Pr. Univ), Marie Mirouze (CR2, IRD), Clémentine Vitte (CR1, CNRS)

Techniques in molecular epigenetics emerged at the genomic scale in the 2000s. The diversity of these approaches with their principle will be briefly presented. From there, it will be considered a reflection on which tools are adapted according to biological questions, study models and material and human constraints. In order to demystify this approach, a demonstration will be carried out with the participants on a technique (McrBC / antibody / BS + electrophoresis, sequencing  ; recent examples MeDIP + WG BS, pipeline of choice).

Interactive course "  Epigenetic basis of phenotypic plasticity and variability  "

Stéphane Maury (Pr. Univ Orléans), Marie Mirouze (CR2, IRD) Clémentine Vitte (CR1, CNRS)

Living organisms are constantly subjected to variations in their environment (biotic and abiotic) which can become harmful. In this context, the set of phenotypes that a genotype can take is called phenotypic plasticity. This process takes place in response to a change in the environment at the individual level. These changes correspond to the plasticity of the individual, they are physiological and / and epigenetic in nature. In recent years, studies in the field of epigenetics in various organisms have focused on phenotypic plasticity and variability. The objective of this interactive course will be to make the participants reflect on the experimental approach which makes it possible to involve epigenetics in these mechanisms and some examples of studies. Working in a small group around a recent research topic will allow you to deepen the notions acquired in class.