Course overview

This course is a theoretical and practical training on the recently emerged field of neuroepigenetics. It will provide an overview of the current concepts and knowledge on the nature and functions of the epigenome in the nervous system, its modes of regulation and its link to brain health and disease. It will combine lectures and hands-on projects to learn about state-of-the-art approaches and methodologies to study how the epigenome is established and modulated by behaviour in rodents and invertebrates, what machinery is involved and what is its causal relationship to functions. It will include methods in behaviour, epigenetics, (epi)genome editing, molecular and cell biology, -omics and bioinformatics.

This course wishes to foster the development of neuroepigenetics as a key discipline in the neurosciences, and train and educate young researchers expected to contribute to the field in the near future. It is intended for PhD students and early career postdocs who wish to acquire good bases and broad knowledge of the field.

Course partner

Course directors

Karine Merienne

Course Director

CNRS – LNCA, University of Strasbourg, France

Angel Barco


Neurosciences Institute (UMH-CSIC), Spain

André Fischer


German Center for Neurodegenerative diseases (DZNE), Germany

Institute of Informatics, University of Warsaw, Poland

Keynote Speakers

Elisabeth Binder – Max Planck Institute of Psychiatry, Munich, Germany
Anne-Laurence Boutillier – LNCA, Strasbourg, France
Goncalo Castelo Branco – Karolinska Institute, Stockholm, Sweden
Johannes Gräff – EPFL, Lausanne, Switzerland
Elizabeth A Heller – Penn Epigenetics Institute, Philadelphia, USA
Denes Hnisz – Max Planck Institute for Molecular Genetics, Berlin, Germany
Aleksandra Pekowska – Dioscuri Center of Chromatin Biology and Epigenomics, Poland


Rafael Alcala Vida – Instituto de Neurociencias UMH-CSIC, Spain
Mykhailo Batiuk – EPFL, Lausanne, Switzerland
Davide Coda – EPFL, Lausanne, Switzerland
Charles Decraene – LNCA, Strasbourg, France
Beatriz del Blanco Pablos – Instituto de Neurociencias UMH-CSIC, Spain
Aleksander Jankowski – Institute of informatics, Warsaw, Poland
Lalit Kaurani – DZNE, Göttingen, Germany
Marta Kullis – IDIBABS, Barcelona, Spain
Stéphanie Legras – IGBMC, Strasbourg, France
Jose Lopez Atalaya – Instituto de Neurociencias UMH-CSIC, Spain
Pierre-Eric Lutz – INCI, Strasbourg, France
Magdalena Machnicka – Institute of informatics, Warsaw, Poland
Marta Alaiz Noya – Instituto de Neurociencias UMH-CSIC, Spain
Isabel Paiva – LNCA, Strasbourg, France
Jose Sanchez-Mut – Instituto de Neurociencias UMH-CSIC, Spain
Sophie Schroeder – DZNE, Göttingen, Germany
Tanya Vavouri – Pujol Research Institute, Badalona, Spain

Course content

Topics & Techniques

State-of-the-art approaches to produce and analyze cell-type-specific epigenomic data in the brain in physiological and disease contexts will be taught, as well as approaches to manipulate the epigenome in brain cells.

  • ChIP seq
  • CUT & Tag seq
  • ATAC seq
  • Single nuclei DNA methylome (snmC-seq2)
  • Single nuclei RNA seq
  • Sample preparation for simultaneous RNAseq, WGBSseq and/or singe-nuclei ATAC-RNAseq (multiome)
  • Design, production and manipulation of epi-editing tools using viral constructs and CRISPR system, and analysis of transcriptional changes at targeted loci
  • Mouse brain subregion dissection, tissue sectioning
  • Fluorescently activated nuclear sorting (FANS) of neuronal and non-neuronal cell populations from mouse brain tissue
  • Isolation of glial cells (astrocytes) from mouse brain tissue using magnetic beads (MACS)
  • RNAscope
  • Confocal microscopy
  • Primary cultures of hippocampal neurons.


Project 1: Cell-type-specific epigenetic profiling using Fluorescence-Activated Nuclear Sorting (FANS) from brain tissue

Project 2: Astrocyte epigenome of mouse hippocampus

Project 3: Transcriptomic profiling of adult mouse brain tissue using 10X Genomics single-nuclei RNA-sequencing

Project 4: Cell type-specific detection of lncRNAs in the mouse brain using RNAscope and immunofluorescence

Project 5: Investigation of single cell DNA methylome landscape of cortical brain cells

Project 6: Cell-type and brain-region specific epigenetic manipulation in Alzheimer’s disease models

Project 7: CRISPR-dCas9 systems for targeted epigenetic repression

Project 8: Epigenome editing technology based on the CRISPR/dCas9 system.

Computational projects: State-of-the-art approaches for bioinformatic analysis and interpretation of the next generation sequencing (NGS) data obtained in the epigenomic experiments covered in the first block.

Bordeaux School of Neuroscience, France

The Bordeaux School of Neuroscience is part of Bordeaux Neurocampus, the Neuroscience Department of the University of Bordeaux. Christophe Mulle, its current director, founded it in 2015. Throughout the year, renowned scientists, promising young researchers and many students from any geographical horizon come to the School.
The school works on this principle: training in neuroscience research through experimental practice, within the framework of a real research laboratory.

Their dedicated laboratory (500m2), available for about 20 trainees, is equipped with a wet lab, an in vitro and in vivo electrophysiology room, IT facilities, a standard cellular imaging room, an animal facility equipped for behavior studies and surgery and catering/meeting spaces. They also have access to high-level core facilities within the University of Bordeaux. They offer their services to international training teams who wish to organize courses in all fields of neuroscience thanks to a dedicated staff for the full logistics (travels, accommodation, on-site catering, social events) and administration and 2 scientific managers in support of the experimentation.


Fee : 3.500 € (includes tuition fee, accommodation and meals)

Applications closed on 5th September 2022

The CAJAL programme offers 4 stipends per course (waived registration fee, not including travel expenses). Please apply through the course online application form. In order to identify candidates in real need of a stipend, any grant applicant is encouraged to first request funds from their lab, institution or government.

Kindly note that if you benefited from a Cajal stipend in the past, you are no longer eligible to receive this kind of funding. However other types of funding (such as partial travel grants from sponsors) might be made available after the participants selection process, depending on the course.

Our partner, ERA-NET NEURON, will also offer grants to participants who are part of an ERA-NET Neuron research group. Please indicate in the application form if you are a member of the network.

Course sponsors

Thanks to Bordeaux University Platforms