Project

Back to overview

Chromatin Organization and Transcriptional Regulation of Axon Guidance Decision

Applicant Fabre Pierre
Number 174032
Funding scheme Ambizione
Research institution Dépt des Neurosciences Fondamentales Faculté de Médecine Université de Genève
Institution of higher education University of Geneva - GE
Main discipline Genetics
Start/End 01.10.2017 - 30.09.2021
Approved amount 1'027'415.00
Show all

All Disciplines (2)

Discipline
Genetics
Embryology, Developmental Biology

Keywords (6)

Gene regulation; Cell-type specification; Central nervous system; Chromatin organization; Enhancer; Single-cell transcriptomics

Lay Summary (French)

Lead
Au cours du développement du système nerveux, les neurones se positionnent et se connectent à leurs cibles pour intégrer de grands réseaux fonctionnels. Or chaque neurone est unique et les processus de différenciation se font sous l’influence de gènes exprimés de façon spécifique et contrôlés par des éléments ‘non codants’ dans des zones encore méconnues du génome. Dans ce projet le but est de dévoiler la structure et la dynamique de ces éléments pour comprendre la logique de régulation des gènes agissant sur la différenciation neuronale.
Lay summary

Contenu et objectifs du travail de recherche

Il a été montré par le passé que la régulation des gènes est à la base de la diversité neuronale. Pour mieux comprendre la logique utilisée par les progéniteurs pour se différencier au bon endroit, au bon moment et dans de bonnes proportions, nous utiliserons la rétine comme modèle car c’est une version simplifiée du système nerveux central. Pour comprendre la régulation des gènes dans ce système, le projet fera appel à de la microscopie et à des approches de génomique fonctionnelle. Cela permettra de mettre en relation les remaniements de structure de la chromatine avec l’expression des gènes importants pour la différenciation des progéniteurs rétiniens. Ce travail minutieux fera appel à la technique de séquençage de cellule unique permettant de discriminer les signatures d’expression de gènes sur des sous-populations de neurones lors de leur développement.

Contexte scientifique et social du projet de recherche

Ce projet relève à la fois de la génétique et de la génomique. Il vise à mettre en relation l’architecture du génome et le contrôle de l’expression des gènes. La découverte d’éléments dit ‘non codants’ du génome pourrait à terme permettre de développer de nouvelles stratégies thérapeutiques pour des maladies neurodégénératives.

Direct link to Lay Summary Last update: 26.09.2017

Responsible applicant and co-applicants

Employees

Publications

Publication
Single-cell transcriptional logic of cell-fate specification and axon guidance in early-born retinal neurons
Lo Giudice Quentin, Leleu Marion, La Manno Gioele, Fabre Pierre J. (2019), Single-cell transcriptional logic of cell-fate specification and axon guidance in early-born retinal neurons, in Development, 146(17), dev178103-dev178103.
Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development
Fabre P. J., Leleu M., Mascrez B., Lo Giudice Q., Cobb J., Duboule D. (2018), Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development, in BMC Biology, 16(1), 101-101.

Datasets

Transcriptome or Gene expression

Author Fabre, pierre
Publication date 20.02.2019
Persistent Identifier (PID) GSE126819
Repository GEO datasets
Abstract
Application of single-cell sequencing C1 to obtain neural retinal transcriptomes. 800 single-cell transcriptomes from E15.5 Sert-Cre developing retinas.

Expression profiling by high throughput sequencing

Author Fabre, Pierre
Publication date 23.08.2019
Persistent Identifier (PID) GSE122466
Repository GEO datasets
Abstract
Examination of two batches for a total of 5347 single-cell transcriptomes from E15.5 C57Bl/6 developing retinas.

Single-cells transcriptomes of mouse developing forelimbs

Author Fabre, Pierre
Publication date 24.08.2018
Persistent Identifier (PID) GSE114748
Repository GEO datasets
Abstract
Single-cells transcriptomes from Hoxd11::GFP forelimbs with micro-dissection of autopod and zeugopod at embryonic day 12 (E12.5). Dissociated single-cells were obtained from eight Hoxd11::GFP forelimbs micro-dissected at E12.5. Cells with the highest level of GFP fluorescence (top 20%) were sorted using an Astrios cell sorter with a 100-μ m nozzle. 75bp reads were uniquely mapped to the latest Mus Musculus reference genome (mm10) and the ERCC sequences using bowtie2 in local mode.

Collaboration

Group / person Country
Types of collaboration
Cepko Lab / Harvard Medical School United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
La Manno lab /EPFL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Andrey Lab / University of Geneva Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
Xin Xhang lab / Columbia University United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
GECF / EPFL Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Exchange of personnel
Jabaudon / University of Geneva Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Research Infrastructure

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
2nd Bioinfo@EPFL annual meeting Poster Cell Fate Specification and axon guidance in early born retinal neurons revealed by single-cell transcriptomic 23.05.2019 EPFL, Switzerland Lo Giudice Quentin;
Annual Meeting of the Swiss Society of Neuroscience Poster Progressive production of retinal neuron diversity during their axonal projection to the developing thalamus 01.02.2019 Campus Biotech, Geneva, Switzerland Lo Giudice Quentin; Fabre Pierre;


Knowledge transfer events

Active participation

Title Type of contribution Date Place Persons involved
Semaine du Cerveau Performances, exhibitions (e.g. for education institutions) 11.03.2019 Geneva, Switzerland Lo Giudice Quentin; Fabre Pierre;


Communication with the public

Communication Title Media Place Year
Media relations: print media, online media La médecine de l'oeil va progresser grâce à des chercheurs genevois Tribune de Genève Western Switzerland 2019
Media relations: radio, television La naissance de la vision RTS radio (CQFD) Western Switzerland 2019
New media (web, blogs, podcasts, news feeds etc.) The birth of vision The Node International 2019
New media (web, blogs, podcasts, news feeds etc.) The borth of vision, from the retina to the brain Science Daily International 2019

Awards

Title Year
iGE3 PhD Salary Award 2019

Abstract

During the development of the brain, the precise expression of factors guiding axon trajectories is key to establishing functional neuronal circuits. These processes are particularly well described in the mouse visual system but little is known about the regulatory logic behind it. To better understand how gene regulation controls the circuit connectivity of retinal neurons, my research project will combine imaging and genome-wide approaches using the mouse retina as a model system. The principal aim of this research is to define the role of chromatin architecture in controlling the expression of genes coding for specific axon guidance receptors and cues to ensure the correct pathfinding of axonal trajectories.The wiring of the retina to the brain requires retinal axons to cross the optic chiasm. However, in humans and mice a subset of the projections, called ipsilateral axons, are repelled and do not cross the chiasm, a segregation that participates in the establishment of binocular vision. This binary outcome represents an excellent paradigm to study axonal guidance decisions. Over the last two decades, the principal genes involved in the crossing of ipsilateral retinal ganglion cell (RGC) axons at the optic chiasm have been identified (Petros et al., 2008). However, the upstream regulatory mechanisms that control the expression of these key guidance genes are unknown. To identify and characterize this regulatory logic, I will prioritize three complementary research axes. First, I will identify, at the single-cell level in the developing mouse retina, the spatio-temporal regulatory signature of the RGCs as they send their axons and make their binary choice. This will be done primarily using single-cell RNA-Seq analysis of wild type retinae and FACS-sorted populations. Second, I will define the mechanisms of enhancer dynamics and chromatin remodeling that controls this spatio-temporal gene expression during retinal axon guidance. To do so I will combine the latest genetics tools, genomics (ATAC-Seq) and super-resolution microscopy (STORM), to describe the link between chromatin structure and the cell fate decisions that trigger precise axonal trajectories. Finally, I will perform functional analyses by modulating the gene networks through their regulatory landscape to impair and/or restore axon guidance choices. Employing genetic strategies previously used during both my PhD and postdoctoral fellowship, I will take advantage of the easily accessible nature of the retina to facilitate this work. I will also benefit from the expertise of my host laboratory in the developmental transcriptional regulation of neocortical neurons in conducting this project.Most of the genetic variants associated with complex human traits are located in non-coding regions. Many of them have been mapped to regulatory elements but little is understood about how they control gene function during the development of the nervous system and its perturbations. The aim of this project is to bridge the field of genomics with cutting edge microscopy in order to uncover the functionality and mechanisms of long-range transcriptional regulation during the establishment of retinal and brain wiring. Understanding these processes will open avenues for precise regenerative medicine. As the retina shows potential for targeted correction, I trust this work will enhance our ability to edit specific regions of the genome without distorting the genes themselves.
-