Publications associées à KRAB'n'KAP, DNA methylation and epigenetic memory

Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos

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

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

Cyril David Son-Tuyên Pulver

The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

EPFL2024

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

Fides Zenk

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

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Didier Trono, Evaristo Jose Planet Letschert, Wayo Matsushima

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

2024

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

Osmosis-driven stiffening of structured hydrogels

Esther Amstad, Ran Zhao, Alexandra Thoma

Plant cells harness osmotic pressures to stiffen their leaves through strong turgor pressures. Key to this osmosisdriven stiffening is the confinement of liquids within semipermeable membranes that can regulate the transport of water molecules and ions. In ...

Elsevier2024

Near-Room-Temperature Detection of Aromatic Compounds with Inkjet-Printed Plasticized Polymer Composites

Thomas Maeder, Jürgen Brugger, Mohammadmahdi Kiaee

Chemiresistive gas sensors composed of a thermoplastic polymer matrix and conductive fillers offer various advantages for detecting volatile organic compounds (VOCs), including low power consumption due to near-room-temperature operation, high sensitivity, ...

Amer Chemical Soc2024

Monitoring an Emergent Pathogen at Low Incidence in Wastewater Using qPCR: Mpox in Switzerland

Tamar Kohn, Timothy R. Julian

Wastewater-based epidemiology offers a complementary approach to clinical case-based surveillance of emergent diseases and can help identify regions with infected people to prioritize clinical surveillance strategies. However, tracking emergent diseases in ...

2024

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Christina Ernst

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Nature Portfolio2024

Verification of the Fourier-enhanced 3D finite element Poisson solver of the gyrokinetic full-f code PICLS

Stephan Brunner, Laurent Villard, Alberto Bottino, Moahan Murugappan

We introduce and derive the Fourier -enhanced 3D electrostatic field solver of the gyrokinetic full -f PIC code PICLS. The solver makes use of a Fourier representation in one periodic direction of the domain to make the solving of the system easily paralle ...

Elsevier2024

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Christina Ernst

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Nature Portfolio2024

Anti-miR-873-5p improves alcohol-related liver disease by enhancing hepatic deacetylation via SIRT1

Kristina Schoonjans, Petar Petrov

Background & Aims: Current therapies for the treatment of alcohol-related liver disease (ALD) have proven largely ineffective. Patients relapse and the disease progresses even after liver transplantation. Altered epigenetic mechanisms are characteristic of ...

Elsevier2024

A Cluster of Evolutionarily Recent KRAB Zinc Finger Proteins Protects Cancer Cells from Replicative Stress–Induced Inflammation

Didier Trono, Priscilla Turelli, Sandra Eloise Kjeldsen, Cyril David Son-Tuyên Pulver, Evaristo Jose Planet Letschert, Filipe Amândio Brandão Sanches Vong Martins, Olga Marie Louise Rosspopoff, Joana Carlevaro Fita, Romain Forey, Florian Huber

Heterochromatin loss and genetic instability enhance cancer progression by favoring clonal diversity, yet uncontrolled replicative stress leads to mitotic catastrophe and inflammatory responses that promote immune rejection. KRAB domain-containing zinc fin ...

2024

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Maria Brbic, Ziang Li

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

Nature Portfolio2024

Dual-frame optimization for informationally complete quantum measurements

Ivano Tavernelli

Randomized measurement protocols such as classical shadows represent powerful resources for quantum technologies, with applications ranging from quantum state characterization and process tomography to machine learning and error mitigation. Recently, the n ...

2024

Exploring High-Performance and Energy-Efficient Architectures for Edge AI-Enabled Applications

Joshua Alexander Harrison Klein

The desire and ability to place AI-enabled applications on the edge has grown significantly in recent years. However, the compute-, area-, and power-constrained nature of edge devices are stressed by the needs of the AI-enabled applications, due to a gener ...

EPFL2024

A chemical biology approach to decipher chromatin ubiquitylation by RNF168

Pauline Franz

DNA damage signaling following DNA double-strand breaks (DSBs) involves numerous regulating proteins, which dynamically recognize ('read') and alter ('write' or 'erase') histone post-translational modifications (PTMs). Among these PTMs, the ubiquitin syste ...

EPFL2024

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

Statistical learning quantifies transposable element-mediated cis-regulation

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

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

KRAB zinc finger proteins link heterochromatin maintenance to replicative stress and inflammation in diffuse large B-cell lymphoma

Filipe Amândio Brandão Sanches Vong Martins

Genomic instability enhances cancer progression by favoring clonal diversity, yet uncontrolled replicative stress can lead to mitotic catastrophe and inflammatory responses promoting immune rejection. KRAB-containing zinc finger proteins (KZFPs) are epigen ...

EPFL2023