M2 Genetics, Genomics, Epigenetics and Evolution (GenE2)

Sébastien BLOYER (PU UPSay I2BC) Benoit MOINDROT (MCU UPSay I2BC) Sophie NETTER (MCU UVSQ I2BC) Conférenciers invités.

This course is organized as a 1-week scientific symposium, with lectures/conferences held by invited speakers. During the conference, a group of 3-4 students will play the role of ‘chairman’: They will be ask to (1) introduce the invited speaker, (2) provide a general introduction of the research area that will later be extensively developed by the invited speaker, (3) lead the discussion and animate the debate between the speaker and the audience. Thus, besides new scientific knowledge acquired during the lectures, the students will acquire and develop know-hows in synthetic presentation of a new topic, public speaking and animation with the audience. The student will be evaluated based on their active implication during the course, and based on their ability to present, using a few experiments from research articles, an epigenetic phenomenon that has not been covered during the course [oral exam organized as a mini-symposium].

This course is organized as a scientific symposium, with lectures held by invited researchers expert in the field of epigenetics, epigenomics and/or non-coding RNAs.
Many aspects of epigenetic processes and phenomena will be covered, such as the control of gene expression, genomic imprinting, X chromosome inactivation, stem cells pluripotency, epigenetic memory and reprogramming, in connection with environmental and/or epigenetic diseases.
The recent advances in cancer single cell epigenomics and 3D genome organization will also be addressed. The focus will be laid on the implication of non-coding RNAs in epigenetic mechanisms, and more particularly in the inter- and trans-generational inheritances of the epigenetic information.
At the end of this course, the students should be able to:
(1) Name, describe and discuss the role of non-coding RNAs in the trans- generational inheritance of the epigenetic information and the different epigenetics layers impacting on cell/tissue identity.
(2) Analyze and interpret epigenetic and epigenomic data from research articles and reviews
(3) Deliver a concise, informative and structured presentation on an epigenetic phenomenon.

Basic concepts in Genetics, Epigenetics and Genomics. Basic knowledge on high-throughput sequencing methods and epigenetic mechanisms.

Books available at Paris Saclay libraries: - Epigenetics by C. David Allis, Marie-Laure Caparros, Thomas Jenuwein and Danny Reinberg - Epigenetics, Nuclear Organization and Gene Function with Implications of Epigenetic Regulation and Genetic Architecture for Human Development and Health by Lucchesi and John C.

Web links : - EpiGensSys European Network Website: http://www.epigenesys.eu/fr/ - Edith Heard’s lectures at the Collège de France (in French): https://www.college-de-france.fr/site/en-edith-heard/_course.htm.

Octobre.

ORSAY - GIF-SUR-YVETTE

Pierre CAPY, Cécile FAIRHEAD, Christine DILLMANN, Judith LEGRAND, Antoine BRANCA, Gaëlle LELANDAIS, Elodie MARCHADIER, Benoit MOINDROT, Pierre GROGNET, Invited speakers.

Find more information on our Website: www.gene2.fr This hands-on workshop takes place in several stages: - ChIP-Seq practical workshop (one week): Design and realize a chromatin immunoprecipitation experiment. During this first part, students will learn about the design of an experiment and the acquisition of high-throughput sequencing data by performing a ChIP experiment, then pre- and post-sequencing validation by qPCR - Bioanalysis and statistical in silico workshop (three weeks): analyze transcriptomic (RNA-Seq) and epigenomic (ChIP-Seq ) data sets. Manipulate FastQ files: transfer, control of quality, filter, map onto reference genome... - Conferences from scientists; visit of the Genoscope at Evry and the I2BC NGS platform at Gif-sur-Yvette - Throughout the workshops, students will be tutored by experts in NGS, biostatistics, data analysis and bioinformatics.

High throughput sequencing has revolutionized biology and is extending to new disciplinary fields (personalized medicine, genetic diseases, cancers, forensic science, etc). During this course, students will learn the basics of Big Data manipulation and analysis and will be able to:
-Describe the experimental techniques to achieve ChIP-seq experiments
-Manipulate high-throughput sequencing files. Choose, set parameters for, and execute software packages for data analysis. Perform sequence alignments, filtering, normalization and quality control. Master the different steps of the differential analysis of RNA-Seq data to sort out differentially expressed genes. Analyse ChIp-Seq data and perform peak-calling
-Computerize and concatenate bioinformatics tools to create workflows
-Choose the apropriate statiscal model and the R package to analyse and correlate the data sets, according to their structure
-Execute clustering of the data (hierarchical clustering, PCA...)
-Analyze and interpret the experimental results, formulate conclusions or hypotheses from these data. Discuss biases, limitations and errors
-Choose the appropriate graphs, and draw figures to visualize high-throughput data.

The BigData workshop is intended for students in biology, medicine, pharmacy or any other scientific background, incling PhD Students who wish to acquire skills in the design, manipulation, processing and analysis of high-throughput sequencing data (genomics, transcriptomics, epigenomics, genotyping, …). No prior computer or statistical training is required.

None.

Septembre - Novembre - Décembre.

ORSAY - EVRY - GIF-SUR-YVETTE

Myriam Harry, Amandine Cornille , Emmanuelle Baudry, Dominique de Vienne, Didier Casane, Marianne Elias, Fanny Hartmann, Arnaud Le Rouzic, Nicolas Pollet, Stéphane Nicolas.

Pedagogical methods (face-to-face, non-face-to-face, internship, etc.): face-to-face (courses and conferences) and non-face-to-face (working independently on the development of a scientific project).

Knowledge test procedures: Students are evaluated using a written report and an oral presentation.

The first part of the unit begins with reminders in population genetics and quantitative genetics followed by conferences illustrating different areas of evolutionary genomics. The conferences draw on examples of current research to illustrate both the fundamental and more applied aspects of evolutionary genomics, such as varietal selection methods based on genomics in agronomy, genomics of disease vector species in humans, predictive medicine and environmental genomics.
The second part of the EU consists of each student writing a research project in the field of evolutionary genomics on a theme chosen by the student. The students will be inspired by the format of the responses to the calls for projects of the ANR, the National Research Agency and will be supported in their approach by the teachers responsible for the EU.
At the end of this course, students will be able to
- describe and assess genetic diversity at different scales and link these diversities together
- formulate a scientific question in evolutionary genomics and propose an adapted methodology (sampling, analysis tools, data processing) to answer it
- critically analyze research work
- design and write a research project.

Genomes, Phenotypes, Populations is intended for students wishing to deepen their knowledge of evolutionary genomics and gain first-hand experience in creating an original research project in this field. Prior training in population genetics and evolutionary biology will be appreciated but non-mandatory.

None.

Octobre.

ORSAY - GIF-SUR-YVETTE

Fabrice Confalonieri (PU UPSay), Stéphanie Bury-Moné (PU UPSay), and invited speakers according to the selected research topics.

Conferences by specialists. Round table with students.

This teaching unit aims to highlight recent advances in functional genomics, including big Data in Biology. The speakers, specialists in this field of research, will present the most recent scientific data relating to comparative genomics, metagenomics, (meta)transcriptomics, metabolomics, proteomics, the analysis of interactomes and applications in medicine. Another objective of this teaching unit is to connect scientific questions asked and the best method(s) to use to reach the goals. Round tables, between students and researchers, will be organized to discuss the impact of the knowledge acquired through global approaches on new emerging concepts related to the gene and to pervasive transcription. Students will also present their own review of a theme they will choose during a one-day mini-symposium.

Basic concepts in Genetics and Genomics. Basic knowledge about gene structure and genome organisation in prokaryotes and eukaryotes.

Octobre.

ORSAY - GIF-SUR-YVETTE

NA.

Students will choose optional teaching units on the themes that they wish, in accordance with organizers. They can choose one 6 ECTS Unit or two 3 ECTS units.

Novembre - Décembre.

Fabrice Confalonieri (PU UPSay), Cécile Fairhead (PU UPSay), and invited speakers according to the selected research topics.

Conferences by specialists in the field. Students will present a bibliographical analysis on one of the themes addressed by the speakers.

This teaching unit consists of scientific lectures/conferences by specialists in the field, about the mechanisms involved in the stability and evolution of genomes, and the methods to study these topics including : the "3Rs" (Replication, Recombination and Repair of DNA), the chromosome/nucleoid structure into macro- and microdomains, programmed mitotic rearrangements and meiotic recombination events, experimental evolution, genetic drift, selection, speciation, comparison between Neandertal and Homo sapiens sapiens genome...

Basic concepts in Genetics, Genomics and Evolution. Basic knowledge about gene structure and genome organisation in prokaryotes and eukaryotes.

Octobre.

ORSAY - GIF-SUR-YVETTE

C. Fairhead, S. Bloyer, P. Capy and invited jury members.

Students will spend 6 months as interns in the laboratory of their choice (academia or private company) from January to June. They will present their first results in March in front of the organizers. At the end of their internship, they will write a scientific report and pass an oral defense.

The internship allows students to get familiar with various experimental approaches as well as the daily activities of a research team.

During the internship, the students participate in an ongoing research project under the guidance of laboratory staff scientists or engineers. They attend lab meetings and conferences. They are introduced to the health and safety regulation. They acquire and analyze experimental data. They have to synthetize their results in the form of a written report and an oral defense.

At the end of this teaching unit, the student will be able to:

- apply to research teams

- integrate a research team and participate in its activities

- follow Health and Safety rules

- to carry out a scientific experiment and integrate the controls required for its interpretation.

- write a laboratory notebook

- analyze critically the results obtained

- synthesize and present a scientific research process and the results obtained in oral and written form.

Janvier - Février - Mars - Avril - Mai - Juin.