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Felix Naef

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Related publications (75)

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Genotypic features of lentivirus transgenic mice

Didier Trono, Felix Naef, Denis Duboule, Marc-Olivier Sauvain, Frédéric Schütz

Lentivector-mediated transgenesis is increasingly used, whether for basic studies as an alternative to pronuclear injection of naked DNA or to test candidate gene therapy vectors. In an effort to characterize the genetic features of this approach, we first ...

American Society for Microbiology2008

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Mohan Vamsi Nallapareddy, Pierre Vandergheynst, Felix Naef, Cédric Gobet, Francesco Craighero

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

PMLR2024

Single Live Cell Monitoring of Protein Turnover Reveals Intercellular Variability and Cell-Cycle Dependence of Degradation Rates

Felix Naef, David Michael Suter, Eric Paquet, Andrea Brigitta Alber

Cells need to reliably control their proteome composition to maintain homeostasis and regulate growth. How protein synthesis and degradation interplay to control protein expression levels remains unclear. Here, we combined a tandem fluorescent timer and pu ...

CELL PRESS2018

Quantitative Analysis and Modeling Probe Polarity Establishment in C. elegans Embryos

Felix Naef, Pierre Gönczy, Coralie Busso, Simon Blanchoud

Cell polarity underlies many aspects of metazoan development and homeostasis, and relies notably on a set of PAR proteins located at the cell cortex. How these proteins interact in space and time remains incompletely understood. We performed a quantitative ...

Cell Press2015

Low-dimensional dynamics of two coupled biological oscillators

Felix Naef, Eric Paquet, Colas Noé Droin

The circadian clock and the cell cycle are two biological oscillatory processes that coexist within individual cells. These two oscillators were found to interact, which can lead to their synchronization. Here, we develop a method to identify a low-dimensi ...

NATURE PUBLISHING GROUP2019

Memory and relatedness of transcriptional activity in mammalian cell lineages

Felix Naef, David Michael Suter, Nicholas Edward Phillips, Aleksandra Mandic

Phenotypically identical mammalian cells often display considerable variability in transcript levels of individual genes. How transcriptional activity propagates in cell lineages, and how this varies across genes is poorly understood. Here we combine live- ...

Nature Research2019

Oscillating and stable genome topologies underlie hepatic physiological rhythms during the circadian cycle

Felix Naef, Jake Yeung, Jérôme Mermet

The circadian clock drives extensive temporal gene expression programs controlling daily changes in behavior and physiology. In mouse liver, transcription factors dynamics, chromatin modifications, and RNA Polymerase II (PolII) activity oscillate throughou ...

2021

Relationship between estrogen receptor alpha location and gene induction reveals the importance of downstream sites and cofactors

Felix Naef, Mauro Delorenzi

BACKGROUND: To understand cancer-related modifications to transcriptional programs requires detailed knowledge about the activation of signal-transduction pathways and gene expression programs. To investigate the mechanisms of target gene regulation by hum ...

BioMed Central2009

Mammalian genes are transcribed with widely different bursting kinetics

Felix Naef, David Michael Suter

In prokaryotes and eukaryotes, most genes appear to be transcribed during short periods called transcriptional bursts, interspersed by silent intervals. We describe how such bursts generate gene-specific temporal patterns of messenger RNA (mRNA) synthesis ...

American Association for the Advancement of Science2011

Cross-regulatory circuits linking inflammation, high-fat diet, and the circadian clock

Felix Naef, Jake Yeung, Frédéric Bruno Martin Gachon

Mammalian physiology resonates with the daily changes in the external environment, allowing processes such as rest-activity cycles, metabolism, and body temperature to synchronize with daily changes in the surroundings. Studies have identified the molecula ...

COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT2018

Non-Circadian Expression Masking Clock-Driven Weak Transcription Rhythms in U2OS Cells

Felix Naef, Laura Symul

U2OS cells harbor a circadian clock but express only a few rhythmic genes in constant conditions. We identified 3040 binding sites of the circadian regulators BMAL1, CLOCK and CRY1 in the U2OS genome. Most binding sites even in promoters do not correlate w ...

Public Library of Science2014

Systems Chronobiology: Global Analysis of Gene Regulation in a 24-Hour Periodic World

Felix Naef, Jake Yeung, Jérôme Mermet

Mammals have evolved an internal timing system, the circadian clock, which synchronizes physiology and behavior to the daily light and dark cycles of the Earth. The master clock, located in the suprachiasmatic nucleus (SCN) of the brain, takes fluctuating ...

Cold Spring Harbor Lab Press, Publications Dept2017

Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver

Felix Naef, Cédric Gobet, Benjamin Dieter Weger, Clémence Yumie Syloun Hurni

In eukaryotes, RNA is synthesised in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject to temporal regulation during the circadian cycle, resulting in daily fluctuations of ...

PUBLIC LIBRARY SCIENCE2022

A chemostat array enables the spatio-temporal analysis of the yeast proteome

Michaël Unser, Sebastian Maerkl, Felix Naef, Ricard Delgado Gonzalo, Arun Stephen Rajkumar, Nicolas Dénervaud, Johannes Becker

Observing cellular responses to perturbations is central to generating and testing hypotheses in biology. We developed a massively parallel microchemostat array capable of growing and observing 1,152 yeast-GFP strains on the single-cell level with 20 min t ...

National Academy of Sciences2013

Space-time logic of liver gene expression at sub-lobular scale

Felix Naef, Colas Noé Droin, Clémence Yumie Syloun Hurni

The mammalian liver is a central hub for systemic metabolic homeostasis. Liver tissue is spatially structured, with hepatocytes operating in repeating lobules, and sub-lobule zones performing distinct functions. The liver is also subject to extensive tempo ...

NATURE RESEARCH2021

V-ATPase/TORC1-mediated ATFS-1 translation directs mitochondrial UPR activation in C. elegans

Johan Auwerx, Kristina Schoonjans, Felix Naef, Xiaoxu Li, Yang Li, Hao Li, Jia Liu, Yan Liu, Wen Gao, Amélia Lalou, Nagammal Neelagandan

To adapt mitochondrial function to the ever-changing intra- and extracellular environment, multiple mitochondrial stress response (MSR) pathways, including the mitochondrial unfolded protein response (UPRmt), have evolved. However, how the mitochondrial st ...

Rockefeller University Press2022

Rhythms of the Genome: Circadian Dynamics from Chromatin Topology, Tissue-Specific Gene Expression, to Behavior

Felix Naef, Jake Yeung

Circadian rhythms in physiology and behavior evolved to resonate with daily cycles in the external environment. In mammals, organs orchestrate temporal physiology over the 24-h day, which requires extensive gene expression rhythms targeted to the right tis ...

ELSEVIER SCIENCE LONDON2018

Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver

Felix Naef, Frédéric Bruno Martin Gachon, Cédric Gobet, Benjamin Dieter Weger, Nagammal Neelagandan

Translation depends on messenger RNA (mRNA)-specific initiation, elongation, and termination rates. While translation elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here we combined ribosome and transfer RNA (tRNA) pr ...

National Academy of Sciences2020

Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome

Felix Naef, Carlos Canto Alvarez, Frédéric Bruno Martin Gachon, Loïc Dayon, Daniel Alain Dominique Marie Mauvoisin, Joanna Ratajczak, Jingkui Wang

Lysine acetylation is involved in various biological processes and is considered a key reversible post-translational modification in the regulation of gene expression, enzyme activity, and subcellular localization. This post-translational modification is t ...

Elsevier2017

The Circadian Clock Coordinates Ribosome Biogenesis

Felix Naef, Frédéric Bruno Martin Gachon, Laura Symul

Biological rhythms play a fundamental role in the physiology and behavior of most living organisms. Rhythmic circadian expression of clock-controlled genes is orchestrated by a molecular clock that relies on interconnected negative feedback loops of transc ...

Public Library Science2013