Publications associées à Unité du Prof. Gräff

Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems

Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the epigenetic mechanisms underlying human cell diversity has been di ...

Nature Portfolio2024

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Beat Fierz, Pauline Franz

Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene ...

Academic Press Ltd- Elsevier Science Ltd2024

Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos

Fides Zenk

Constitutive heterochromatin is essential for transcriptional silencing and genome integrity. The establishment of constitutive heterochromatin in early embryos and its role in early fruitfly development are unknown. Lysine 9 trimethylation of histone H3 ( ...

Springernature2024

A theory of memory consolidation and synaptic pruning in cortical circuits

Georgios Iatropoulos

Over the course of a lifetime, the human brain acquires an astonishing amount of semantic knowledge and autobiographical memories, often with an imprinting strong enough to allow detailed information to be recalled many years after the initial learning exp ...

EPFL2023

Noninvasive deep brain stimulation to modulate human behavior by means of transcranial temporal interference electrical stimulation

Elena Beanato

All functions we use in our everyday life depend on a complex interplay between both cortical and subcortical brain areas, communicating in between each others. When a region is affected by either an accident, aging or neurodegenerative diseases, the whole ...

EPFL2023

Chromatin modules and their implication in genomic organization and gene regulation

Bart Deplancke, Guido Van Mierlo, Judith Franziska Kribelbauer

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

ELSEVIER SCIENCE LONDON2023

Statistical learning quantifies transposable element-mediated cis-regulation

Didier Trono, Evaristo Jose Planet Letschert, Julien Léonard Duc, Cyril David Son-Tuyên Pulver, Alexandre Coudray, Julien Paul André Pontis, Delphine Yvette L Grun, Shaoline Sheppard, Raphaël Gérard Théodore Michel Marie de Deloÿe et Fourcade de Fondeville

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

2023

Deciphering the molecular events leading to the global restoration of the chromatin landscape during mitotic exit

Silja Michelle Placzek

Two fundamental properties of embryonic stem cells (ESCs) are their ability to self-renew and differentiate into all somatic cell types. Maintenance of their identity faces major challenges when transitioning through mitosis, as most DNA-binding proteins a ...

EPFL2023

Engram cell connectivity as a mechanism for information encoding and memory function

Maurizio Ferdinando Pezzoli

Information derived from experiences is incorporated into the brain as changes to ensembles of cells, termed engram cells, which allow memory storage and recall. The mechanism by which those changes hold specific information is unclear. Here, we test the h ...

Cell Press2023

Tissue clearing applications in memory engram research

Johannes Gräff, Kwok Yui Reymond Yip

A memory engram is thought to be the physical substrate of the memory trace within the brain, which is generally depicted as a neuronal ensemble activated by learning to fire together during encoding and retrieval. It has been postulated that engram cell e ...

FRONTIERS MEDIA SA2023

Computational models of episodic-like memory in food-caching birds

Wulfram Gerstner, Johanni Michael Brea

How the 'what', 'where', and 'when' of past experiences are stored in episodic memories and retrieved for suitable decisions remains unclear. In an effort to address these questions, the authors present computational models of neural networks that behave l ...

Nature Portfolio2023

Plasticity of sensory representations in the posterior insular cortex during fear learning

Denys Osypenko

Aversively-motivated associative learning allows animals to avoid harm and thus ensures survival. Aversive learning can be studied by the fear learning paradigm, in which an innocuous sensory stimulus like a tone (conditioned stimulus, CS), acquires a nega ...

EPFL2023

A dynamic attractor network model of memory formation, reinforcement and forgetting

Wulfram Gerstner, Chiara Gastaldi, Marta Boscaglia

Empirical evidence shows that memories that are frequently revisited are easy to recall, and that familiar items involve larger hippocampal representations than less familiar ones. In line with these observations, here we develop a modelling approach to pr ...

Public Library Science2023

Face your fears: attenuating remote fear memories by reconsolidation-updating

Johannes Gräff, Bianca Ambrogina Silva

Traumatic events generate some of the most enduring memories, yet little is known about how long-lasting fear memories can be attenuated. In this review, we collect the surprisingly sparse evidence on remote fear memory attenuation from both animal and hum ...

ELSEVIER SCIENCE LONDON2023

Bodily self-consciousness as a framework to link sensory information and self-related components of episodic memory: behavioral, neuroimaging, and clinical evidence

Nathalie Heidi Meyer

The recollection of sensory information and subjective experience related to a personal past event depends on our episodic memory (EM). At the neural level, EM retrieval is linked with the reinstatement of hippocampal activity thought to recollect the sens ...

EPFL2023

Prefrontal engrams of long-term fear memory perpetuate pain perception

Johannes Gräff, Yechao Han

A painful episode can lead to a life-long increase in an individual's experience of pain. Fearful anticipation of imminent pain could play a role in this phenomenon, but the neurobiological underpinnings are unclear because fear can both suppress and enhan ...

NATURE PORTFOLIO2023

Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos

Denis Duboule, Alexandre Gauthier Aurèle Mayran, Hocine Rekaik, Célia Corinne Renée Bochaton, Lucille Delisle, Aurélie Hintermann

Temporal activation of Hox genes in mouse pseudo-embryos in vitro initiates at the anterior part of the cluster and is accompanied by asymmetric loading of cohesin. Posterior CTCF sites then successively act as transient insulators, regulating the timed tr ...

NATURE PORTFOLIO2023

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

Daniele Tavernari, Giovanni Ciriello

Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis-regulatory effect of integrated ...

Wiley2023

Epigenetic plasticity as a signature for memory allocation

Giulia Santoni

Long-lasting memories are stored in a small set of neurons scattered throughout the brain, so-called engram cells. To define a stable engram each region of the brain involved in memory storage recruits between 5 and 20 percent of excitatory neurons. In par ...

EPFL2022